Derivation of hepatic stem cells and mature liver cell types and uses thereof

ABSTRACT

This application describes liver stem cells (LSC), and differentiated hepatocytes, cholangiocytes, and 3D cellular structures derived therefrom. Methods for producing LSC and mature, differentiated hepatocytes and cholangiocytes in culture are provided. Also provided are cell culture systems and cell culture media for producing a homogenous population of liver stem cells that remain in an undifferentiated state over multiple passages in culture. The LSC and methods are useful for producing homogenous populations of hepatocytes and cholangiocytes for downstream applications. The LSC can be transplanted into subjects to treat liver diseases.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is the U.S. National Stage of International Patent Application No.: PCT/SG2016/050270, filed on Jun. 10, 2016, which claims the benefit of priority to Singapore Application No. SG 10201504657Y, filed Jun. 12, 2015, and Singapore Application No. SG 10201504659X, filed Jun. 12, 2015, which are all incorporated by reference herein in their entireties.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED ON A COMPACT DISK

The Sequence Listing written in file 1012194 ST25.txt, created on Jun. 9, 2016, 223,255 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

A Need for Self-Renewable Source of Mature Hepatocytes

The liver is the largest glandular organ in the body and performs multiple critical functions to keep the body pure of toxins and harmful substances. Liver function is mainly contributed by hepatocytes. Hepatocyte is the main cell type for glucose metabolism, lipid metabolism, urea metabolism and detoxification. It produces bile to digest fats; stores glucose, vitamins and iron; converts ammonia to urea and detoxifies the blood to rid it of harmful substances such as alcohol and drugs. In most liver diseases, hepatocytes are progressively loss to the extent where liver function fails and transplantation remains the gold standard of treatment. However, the medical complexity of the procedure coupled with a severe lack of healthy liver grafts creates an urgent need for more sustainable options. Worldwide, the mismatch between liver graft availability and patients waiting for a liver transplant has widened exponentially resulting in more patients dying while on the waiting list. This unmet clinical need has spurred much effort to develop cellular transplantation as an alternative to whole organ transplantation. Beside clinical needs, hepatocytes are constantly used in the industry for in vitro toxicology screens. Drug induced liver injury remains a major hurdle for many drugs in reaching clinical trials and in some cases drugs have been withdrawn from the shelf because of toxicity issues. This in part stems from the limitations of current in vitro hepatocyte toxicity models and mouse toxicity models to predict all forms of drug induced liver injury [1,2]. There is an urgent need for a renewable source of quality hepatocytes for both industrial and clinical applications. Hepatocytes isolated from fresh liver tissue lose their major drug metabolic enzyme Cytochrome p450 (CYP) activity after 24-48 hours of in vitro culture. Currently there is no method available for long term culture of primary hepatocyte, without the loss of their CYP drug metabolism functions. Besides the liver, a plausible renewable source of hepatocytes would be their derivation from pluripotent stem cells. However, these cells at best achieve functional activity of immature fetal hepatocytes which is much lower than mature adult hepatocytes [3]. In contrast, the liver stem cells described herein generate hepatocytes with adult hepatocyte features and the self-renewal capacity makes them a sustainable source of mature liver adult stem cells.

Structure and Cell Types in an Adult Liver

The liver lobule forms the functional basic unit of the liver [4]. Hepatocytes are compacted around a central vein and the portal triad (consisting of the bile ducts, hepatic vein and hepatic artery) are found at the edge of the lobule. While hepatocytes form the majority of the cells in the lobule, several other cells types are essential to form the ductal and vasculature networks, and immune surveillance of the organ. Other major cell types in the liver includes bile duct cells (cholangiocytes), liver sinusoidal endothelial cells, vasculature endothelial cells, immune cells including Pit cells, Kupffer cells and hepatic stellate cells. Within the liver lobules, hepatocytes are distributed to 3 different zones, determined by their proximity to the central vein or the portal triad located at the end of the lobule. Hepatocytes in the different zones are exposed to different niche environments and play specific functional roles in the liver. They can be distinguished by the expression of different markers, glucose and lipid metabolic functions.

Functional Hepatocytes and Cholangiocytes

Hepatocytes are the chief functional cells of the liver. As mentioned previously they perform an astonishing number of metabolic, endocrine and secretory functions. Roughly 80% of the mass of the liver is contributed by hepatocytes. In three dimensions, hepatocytes are arranged in plates that anastomose with one another. The cells are polygonal in shape with one or two prominent nucleoli and their sides can be in contact either with sinusoids (sinusoidal face) or neighboring hepatocytes (lateral faces). Hepatocyte function could be assessed by glucose storage, ion uptake, bile salt secretion, amino acid metabolic function, urea synthesis and drug metabolic function test.

The drug metabolizing function of hepatocytes is mediated by cytochrome P450s (CYPs). CYPs constitute the major enzyme family capable of catalyzing the oxidative biotransformation of most drugs. 90% of drugs are metabolized by six major CYPs (CYP3A4/5, CYP2C9, CYP2C19, CYP1A2, CYP2B6 and CYP2D6) [5]. CYP function can be enhanced by induction with specific drugs. CYP function and drug induction response is a major critical criterion used to assess the functional maturity of lab-made hepatocytes. While hepatocytes have been derived using various methods from embryonic and fetal tissues, the maturity and functionality of these hepatocytes as determined by the activities of the 6 major CYPs and their response to drug induction showed that they were functionally immature [6,13]. Therefore current methods known in the field of deriving hepatocytes do not solve the issue of obtaining large numbers of functionally mature hepatocytes for both industrial and clinical applications.

Besides hepatocytes, bile duct cells (cholangiocytes) are another type of liver parenchymal cell. Cholangiocytes are epithelial cells that line the intra- and extrahepatic ducts of the biliary tree [7]. The main physiologic function of cholangiocytes is modification of hepatocyte-derived bile. Typical cholangiocytes are polarized columnar cells. Their nucleoli are located near the basal membrane. Primary cilia extend from the cholangiocyte apical plasma membrane and into the ductal lumen. Microvilli formed by primary cilia on the apical plasma membrane significantly increase the cholangiocyte surface area. This enhances secretion and ion transport function of cholangiocytes [7]. Microvilli are a major structural characteristic used to assess the maturation of cholangiocytes. Currently, there are no reports of in vitro differentiated cholangiocytes with microvilli structures. Herein, we show that adult stem cells can generate mature cholangiocytes with microvilli.

Multiple Regenerative Cell Source in the Liver

In vivo, the liver is one of the most regenerative organs of the human body [8]. The human liver can lose up to ⅔ of its mass, maintains its critical functions and recover to the original mass within 8-15 days. Studies have shown during the recovery from a partial liver hepatectomy, hepatocytes from all regions of the liver proliferate [8,9], including bile duct cells. Recent lineage tracing experiments have identified proliferative hepatocytes in different regions of the liver, near the central vein [10] or the portal triad [11] during both normal liver homeostasis and liver injuries. Other than hepatocytes, potential proliferative cells have been identified in the bile duct regions that could replenish damage hepatocytes during injury [9,12].

Isolation of Adult Hepatic Stem Cells from the Adult Human Liver

The multi-cellular origin of liver stem cells suggests different methods can be used to isolate and derive stem cells from the liver. The ability to successfully isolate and expand liver stem cells and further differentiate them into functional hepatocytes for meaningful repopulation in an injured liver to deliver clinical benefit has become a top priority for liver stem cell biologists. To date, two groups have reported isolating stem cells from adult liver tissue that could be stably expanded in vitro for the long term. However, the hepatocytes derived from these stem cells are functionally immature and are unsuitable for use in clinical and industrial applications.

The first group (see WO2015/173425 A1) successfully isolated stem cells from liver tissue based on cells expressing 2 key markers, Leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5) and Epithelial cell adhesion molecule (EPCAM). EPCAM expressing cells were embedded in matrigel to form a liver epithelial cell mass. The epithelial cell mass mainly consisted of cells expressing bile duct cell markers Keratin 19 (KRT19), Keratin 7 (KRT7) and EPCAM, suggesting that the origin of the cells was from bile ducts in the liver. While hepatocytes and cholangiocytes could be derived from this epithelial cell mass, no evidence was presented that the cells were mature. The hepatocytes were only shown to exhibit Cytochrome P450, Family 3, Subfamily A, Polypeptide 4 (CYP3A4) activity. This cytochrome activity is highly active in immature hepatocytes derived from embryonic or fetal tissues or stem cells [13]. There is no evidence that the cells exhibited mature Cytochrome P450, Family 2, Subfamily C, Polypeptide 9 (CYP2C9) functions, or that Cytochrome P450 (CYP) activity could be further induced with a drug. Similarly, derived cholangiocytes did not show mature phenotypes such as a polarized cell structure and the presence of cilia on the apical membrane. Thus, there is no evidence that the methods disclosed in WO2015/173425 were capable of generating mature hepatocytes and cholangiocytes.

A second group (see WO2014152321 A1) described isolating adult stem cells from various tissues or organs including stomach, small intestine, colon, intestinal metaplasia, fallopian tube (oviducts), kidney, pancreas, liver, and lung. Their isolated liver stem cell expressed mainly bile duct markers such as KRT7 and KRT19. The liver stem cells were shown to differentiate into Alpha-Fetoprotein (AFP) expressing hepatocytes. AFP is only found in embryonic and fetal immature hepatocytes. This suggested that these stem cells cannot generate fully mature hepatocytes. No metabolic functions were described, and no evidence was presented that the stem cells could differentiate into cholangiocytes. In addition, the in vivo transplantation data presented did not show that the liver stem cell could differentiate into functional hepatocytes in the mouse liver.

BRIEF SUMMARY OF THE INVENTION

The invention provides a method to isolate hepatic stem cells from adult human liver tissue, mouse liver, and fetal liver. The method used only a single media for the isolation and propagation of the liver stem cells. The media and feeder cells for isolating the stem cell could also be used for long term maintenance of these cells, cryopreservation of these cells and subsequent thawing of the cells for continuous culture. Using specific differentiation media, these stem cells could be used to generate both mature and functional hepatocytes and cholangiocytes.

In this application, we demonstrate that hepatic stem cells with a strong hepatocyte gene signature can be isolated. The isolated stem cells described herein expressed very low levels of KRT19 and no detectable KRT7, which distinguishes the stem cells described herein from stem cells known in the art. The stem cells described herein also expressed mature hepatocyte markers such as Hepatocyte Nuclear Factor 3, Beta (HNF3β) and Hepatocyte Nuclear Factor 4, Alpha (HNF4α). We were able to isolate stem cells both from EpCam+ and EpCam− liver cells. More importantly, we showed that the hepatic stem cells can generate hepatocytes that exhibited multiple CYP metabolic activities, including CYP2C9 activity, which is only found in adult hepatocytes. Furthermore, we showed that CYP activities were responsive to drug induction. The bipotent hepatic stem cells could also generate mature cholangiocytes in vitro. The bile duct cells were polarized and cilia can be found on the apical membrane of the cells, showing that the stem cell derived cholangiocytes were highly mature. We describe the first isolation of bipotent hepatic stem cells that are capable of differentiating into mature hepatocytes and mature cholangiocytes.

The methods described herein were used to isolate liver stem cells from mouse and human fetal stem cells (FIG. 6), and could potentially be used to isolate liver stem cells from other mammals from primate to rodent, such as pigs or monkeys. The liver stem cells could also be isolated and derived from both healthy and diseased liver (FIG. 8). The liver diseases includes liver metabolic disease, such as nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH); autoimmune disease, such as primary sclerosing cholangitis (PSC), primary biliary cirrhosis (PBC); infectious disease, such as hepatitis virus infected liver cirrhosis; drug induced acute and chronic liver failure, such as drug induced liver injury (DILI); alcoholic liver cirrhosis and liver cancer, such as hepatocarcinoma (HCC) and cholangiocarcinoma (FIG. 8, Tables 1 and 3).

Liver stem cells were isolated, maintained and cultured using a single serum free media from human liver tissue. The human liver tissue herein can refer to any parts of the liver dissected from diseased or normal and fetal or adult liver. Stem cells were derived, maintained and propagated on fibroblasts that included 3T3J2 cells, Swiss3T3, NIH3T3 and L1 (FIG. 14). The liver stem cells could be surprisingly maintained for more than 19 passages (280 days) in culture without detectable karyotype abnormalities (FIG. 10).

Liver stem cells could be differentiated into two of the major parenchymal cell types in the liver, hepatocytes and bile duct cells (cholangiocytes). These were achieved by specific media for each cell type.

Both liver stem cells and their in vitro differentiated hepatocytes were able to repopulate when transplanted into mouse liver. The transplanted liver stem cells and their differentiated hepatocyte rescued liver function in a drug-induced liver cirrhosis mouse model. This is the first report to show human liver stem cells and their differentiated hepatocytes function in liver regeneration to rescue a liver cirrhosis phenotype.

In one aspect, a liver stem cell is described herein, the liver stem cell comprising the following characteristics:

-   -   (i) expresses at least 1, 2, 3 or 4 of the protein markers         selected from SOX9, HNF4a, HNF3β, and EPCAM;     -   (ii) expresses low levels of KRT19 protein,     -   (iii) does not express detectable protein levels of KRT7 or AFP;         and     -   (iv) does not have a polarized cell phenotype.

In some embodiments, the liver stem cell further expresses 1, 2, 3, 4, or 5 protein markers selected from CD24, PROM1, FOXA3, FOXQ1 and ECAD. The characteristics of the stem cell are maintained in long-term culture, and comprise a normal karyotype after 19 passages in culture.

The liver stem cell can be derived from a mammal, such that the liver stem cell can be a mammalian liver stem cell, a human liver stem cell, a mouse liver stem cell, or a fetal liver stem cell. In some embodiments, the liver stem cell is isolated from a healthy subject. In some embodiments, the liver stem cell is isolated from a mammalian subject with liver disease, wherein the liver disease is selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer. In some embodiments the subject is a human.

In a second aspect, a differentiated hepatocyte derived from a liver stem cell described herein is provided. In some embodiments, the differentiated hepatocyte comprises at least one of the following characteristics:

-   -   (i) expresses the markers HNF4a and ALB;     -   (ii) expresses at least 1, 2, 3, 4, 5, 6, 7 or 8 of the CYP         enzymes selected from CYP3A4, CYP2C9, CYP2B6, CYP1A2, CYP1A1,         CYP2D6, CYP3A7, and CYP2E1;     -   (iii) have at least 1, 2 or 3 of the following functions:         -   a) functional glucose metabolism;         -   b) functional lipid metabolism;         -   c) functional albumin secretion;     -   (vi) indocyanine green (ICG) uptake; and     -   (vii) forms tight junctions when cultured with other         differentiated hepatocytes under conditions sufficient to form         an epithelium.

The differentiated hepatocyte can also express at least one of the terminal differentiation markers PEPCK1 or TAT. The differentiated hepatocyte has inducible CYP function for at least 2, 3, or 4 of the CYPs selected from CYP3A4, CYP2C9, CYP2B6, CYP1A2, CYP1A1, CYP2D6, CYP3A7, and CYP2E1. The differentiated hepatocyte can also store glycogen and uptake low density lipoprotein.

In some embodiments, the differentiated hepatocyte is differentiated from a liver stem cell isolated from a healthy human or from a human with liver disease selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

In another aspect, a differentiated cholangiocyte derived from a liver stem cell described herein is provided. In some embodiments, the differentiated cholangiocyte comprises at least one of the following characteristics:

-   -   (i) expresses the markers KRT19 (Accession no: P08727.4) and         KRT7 (Accession no: P08729.5) and ECAD;     -   (ii) has columnar epithelial cell polarity comprising an apical         region and a basolateral region when cultured with other         differentiated cholangiocytes under conditions sufficient to         form an epithelium;     -   (iii) comprises microvilli on the apical region;     -   (iii) forms biliary duct-like 3 dimensional (3D) structure when         cultured with other differentiated cholangiocytes under         conditions sufficient to form 3D structures.

In some embodiments, the differentiated choloangiocyte is differentiated from a liver stem cell isolated from a healthy human or from a human with liver disease selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

In another aspect, a cell culture system for culturing liver stem cells is provided. In some embodiments, the liver stem cell culture system described herein comprises a plurality of soluble agents in a stem cell culture media and a cellular support capable of providing structural and nutritional support. The cellular support helps maintain the liver stem cells in an adhesion layer. In some embodiments, the plurality of soluble agents comprises:

-   -   at least one growth factor,     -   an enhancer of the (canonical) WNT pathway,     -   a stem cell differentiation inhibitor

The cell culture system can enhance stem cell proliferation and/or prevent stem cell differentiation into mature liver cells. In some embodiments, the system is a BMP (Bone morphogenetic protein) inhibitor-free, and/or HGF (Hepatocyte growth factor)-free, and/or FGF (Fibroblast growth factor)-free system.

In some embodiments, the liver stem cells produced by the cell culture system are characterized by having at least one feature selected from the group consisting of:

-   -   a. when cultured on the cellular support, the liver stem cells         are small and round in shape and clustered together forming a         disk like structure.     -   b. the liver stem cells express low levels of KRT19.     -   c. the liver stem cells are positive for the markers Epithelial         Cadherin (E-CAD), Epithelial Cell Adhesion Molecule (EPCAM),         Hepatocyte Nuclear Factor 4 Alpha (HNF4α), and SRY (Sex         Determining Region Y)-Box 9 (SOX9);     -   d. the liver stem cells are substantially negative for bile duct         differentiation markers, such as KRT7. In some embodiments, less         than 5%, less than 10% or less than 15% of the liver stem cells         expresses KRT7;     -   e. at least about 80%, about 85%, about 90%, or about 95% of the         liver stem cells express a transcription factor for hepatocyte         lineage differentiation, such as HNF4a;     -   f. the liver stem cells comprise homogenous bipotential         progenitor/stem cells; and     -   g. the liver stem cells are capable of developing into mature         adult hepatocytes that express having at least four major         Cytochrome P450 (CYP) functions.

In some embodiments, the cellular support comprises feeder cells. In some embodiments, the growth factor is capable of increasing cell metabolism by assisting the cell in releasing cyclic AMP (adenosine monophosphate).

In some embodiments, the enhancer of the (canonical) WNT pathway activates the beta-catenin pathway. The enhancer of the canonical WNT pathway can be a Wnt agonist. In some embodiments, the Wnt agonist is selected from the group consisting of: a Wnt family member (Wnt-1/Int-1, Wnt-2/Irp (Int-1-related Protein), Wnt-2b/13, Wnt-3/Int-4, Wnt-3a, Wnt-4, Wnt-5a, Wnt-5b, Wnt-6, Wnt-7a, Wnt-7b, Wnt-8a/8d, Wnt-8b, Wnt-9a/14, Wnt-9b/14b/15, Wnt-10a, Wnt-10b/12, Wnt-11, and Wnt-16); an R-spondin family member (R-spondin 1, R-spondin 2, R-spondin 3, and R-spondin 4); Norrin (Norrie Disease Protein or NDP); a Glycogen synthase kinase 3 inhibitor selected from small-interfering RNAs, lithium, kenpaullone, 6-Bromoindirubin-30-acetoxime, SB 216763 (3-(2,4-Dichlorophenyl)-4-(1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione), SB 415286 (4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide; CHIR 99021 (6-[[2-[[4-(2,4-Dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2-pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile), CHIR 99021 trihydrochloride (6-[[2-[[4-(2,4-Dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2-pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile trihydrochloride), Kenpaullone, Indirubin-3′-oxime, MeBIO ((2′Z,3′E)-6-Bromo-1-methylindirubin-3′-oxime) TCS 2002 (2-Methyl-5-[3-[4-(methylsulfinyl)phenyl]-5-benzofuranyl]-1,3,4-oxadiazole), Lithium carbonate, NSC 693868 (1H-Pyrazolo[3,4-b]quinoxalin-3-amine), TCS 21311 (3-[5-[4-(2-Hydroxy-2-methyl-1-oxopropyl)-1-piperazinyl]-2-(trifluoromethyl)phenyl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione), AR-A 014418 (N-[(4-Methoxyphenyl)methyl]-N′-(5-nitro-2-thiazolyl)urea), 3F8 (5-Ethyl-7,8-dimethoxy-1H-pyrrolo[3,4-c]isoquinoline-1,3(2H)-dione), L803 (Peptide KEAPPAPPQSP), A 1070722 (1-(7-Methoxyquinolin-4-yl)-3-[6-(trifluoromethyl)pyridin-2-yl]urea), 10Z-Hymenialdisine, TC-G 24 (N-(3-Chloro-4-methylphenyl)-5-(4-nitrophenyl)-1,3,4-oxadiazol-2-amine), TWS 119 3-[[6-(3-Aminophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]oxyphenol ditrifluoroacetate]), and L803-mts (peptide GKEAPPAPPQSP); and a FRAT-family member (FRAT: frequently rearranged in advanced T-cell lymphomas) and FRAT-derived peptides. In some embodiments, the Wnt agonist is R-spondin 1.

In some embodiments, the stem cell differentiation inhibitor is a TGF-beta inhibitor. In some cases, the TGF-beta inhibitor is selected from the group consisting of A83-01 (3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide) and SB431542 (4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide).

In some embodiments, the growth factor is Epidermal Growth Factor (EGF) and/or thyroid hormone. Thyroid hormone can be selected from the group consisting of 3,3′-5-triiodo-1-thyronine (T3), (S)-thyroxine (T4) and hormones that stimulate cAMP.

In some embodiments, the system further comprises at least one component selected from the group consisting of an extracellular matrix, an agent for activating the Notch pathway, endotoxin, N-acetylcysteine and nicotinamide. In some cases, the agent for activating the Notch pathway is a notch ligand. In some embodiments, the endotoxin is Cholera endotoxin.

In some embodiments, the feeder cell is a fibroblast cell line, such as a mouse or human fibroblast cell line. The mouse fibroblast cell line can be a 3T3J2 feeder cell line.

In some embodiments, the extracellular matrix is matrigel, or a s a growth factor reduced matrigel.

In another aspect, a cell culture system is provided, the cell culture system comprising an extracellular matrix, an EGF, R-spondin1, SB431542, Jagged-1 (amino acid residues 188-204; CDDYYYGFGCNKFCRPR (SEQ ID NO:1), 3,3′-5-triiodo-1-thyronine (T3), Cholera endotoxin, Nicotinamide, N-acetylcysteine and a feeder cell.

In another aspect, a cell culture system is provided, the culture system comprising a growth factor reduced matrigel, an EGF, R-spondin1, SB431542, Jagged-1 (SEQ ID NO:1), 3,3′-5-triiodo-1-thyronine (T3), Cholera endotoxin, Nicotinamide, N-acetylcysteine and a feeder cell.

In another aspect, a cell culture system is provided, the cell culture system comprising a growth factor reduced matrigel, an EGF, R-spondin1, SB431542, Jagged-1 (SEQ ID NO:1), 3,3′-5-triiodo-1-thyronine (T3), Cholera endotoxin, Nicotinamide, N-acetylcysteine and a mouse fibroblast 3T3J2 feeder cell line.

In some embodiments, the concentration of Epidermal Growth Factor (EGF) in the system is from about 5 ng/ml to about 200 ng/ml, or about 10 ng/ml to about 150 ng/ml, or about 35 ng/ml to about 100 ng/ml, or about 40 ng/ml to about 60 ng/ml, or about 41 ng/ml, or about 42 ng/ml, or about 43 ng/ml, or about 44 ng/ml, or about 45 ng/ml, or about 46 ng/ml, or about 47 ng/ml, or about 48 ng/ml, or about 49 ng/ml, or about 50 ng/ml, or about 51 ng/ml, or about 52 ng/ml, or about 53 ng/ml, or about 54 ng/ml, or about 55 ng/ml, or about 56 ng/ml, or about 57 ng/ml, or about 58 ng/ml, or about 59 ng/ml.

In some embodiments, the concentration of R-spondin 1 in the system is from about 100 ng/ml to about 500 ng/ml, or about 110 ng/ml to about 400 ng/ml, or about 150 ng/ml to about 350 ng/ml, or about 200 ng/ml to about 300 ng/ml, or about 230 ng/ml to about 270 ng/ml, or about 235 ng/ml, or about 240 ng/ml, or about 245 ng/ml, or about 250 ng/ml, or about 255 ng/ml, or about 260 ng/ml, or about 265 ng/ml.

In some embodiments, the TGF-beta inhibitor is SB431542. In some embodiments, the concentration of SB431542 in the system is from about 0.1 ng/ml to about 10 ng/ml, or about 0.5 ng/ml to about 8 ng/ml, or about 2 ng/ml to about 7 ng/ml, or about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In some embodiments, the Notch ligand is Jagged-1 CDDYYYGFGCNKFCRPR (SEQ ID NO:1) (Jagged-1 (188-204)). In some embodiments, the concentration of Jagged-1 in the system is from about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In some embodiments, the thyroid hormone is 3,3′-5-triiodo-1-thyronine (T3). In some cases, the concentration of T3 in the system is from about 0.2 μM to about 20 μM, or about 0.1 μM to about 15 μM, or about 1 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM, or about 10 μM, or about 11 μM, or about 12 μM, or about 13 μM, or about 14 μM.

In some embodiments, the concentration of nicotinamide in the system is from about 1 mM to about 50 mM, or about 1 mM to about 25 mM, or about 5 mM to about 15 mM, or about 6 mM, or about 7 mM, or about 8 mM, or about 9 mM, or about 10 mM, or about 11 mM, or about 12 mM, or about 13 mM, or about 14 mM.

In some embodiments, the concentration of N-acetylcysteine in the system is from about 0.1 μM to about 10 μM or about 1 μM to about 10 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In some embodiments, the concentration of Cholera endotoxin in the system is from about 0.01 μM to about 1 μM or about 0.05 μM to about 0.9 μM, or about 0.95 μM, or about 0.1 μM, or about 0.2 μM, or about 0.3 μM, or about 0.4 μM, or about 0.5 μM, or about 0.6 μM, or about 0.7 μM, or about 0.8 μM, or about 0.9 μM.

In another aspect, a cell culture medium for liver stem cells is provided, the cell culture medium comprising: basal media, about 0.1% to about 5% N2, about 0.1% to 5% B27, about 5 ng/ml to about 200 ng/ml EGF, about 25 to about 500 ng/ml R-Spondin 1, about 0.1 μM to about 10 μM SB431542 (4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide), about 0.1 μM to about 10 μM T3 (3,3′,5-Triiodo-L-Thyronine), and about 1 mM to about 50 mM Nicotinamide. In some embodiments, the basal medium is advanced F12/DMEM reduced serum medium.

In some embodiments, the concentration of R-Spondin 1 in the culture medium is about 25 ng/ml to about 500 ng/ml, or about 100 ng/ml to about 500 ng/ml, or about 110 ng/ml to about 400 ng/ml, or about 150 ng/ml to about 350 ng/ml, or about 200 ng/ml to about 300 ng/ml, or about 230 ng/ml to about 270 ng/ml, or about 25 ng/ml, or about 50 ng/ml, or about 100 ng/ml, or about 125 ng/ml, or about 235 ng/ml, or about 240 ng/ml, or about 245 ng/ml, or about 250 ng/ml, or about 255 ng/ml, or about 260 ng/ml, or about 265 ng/ml, or about 500 ng/ml.

In some embodiments, the culture medium further comprises Jagged-1 (SEQ ID NO:1), wherein the concentration of Jagged-1 in the culture medium is about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 0.1 μM, or about 0.5 μM, or about 1.0 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In some embodiments, the culture medium further comprises Cholera enterotoxin (CTX), wherein the concentration of CTX in the culture medium is between about 0.01 μM and about 1 μM, or about 0.05 μM to about 0.9 μM, or about 0.05 μM, or about 0.1 μM, or about 0.2 μM, or about 0.3 μM, or about 0.4 μM, or about 0.5 μM, or about 0.6 μM, or about 0.7 μM, or about 0.8 μM, or about 0.9 μM.

In some embodiments, the culture medium further comprises N-Acetyl-Cysteine (NAC), wherein the concentration of NAC in the culture medium is about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In another aspect, a kit is provided, the kit comprising the components of the liver stem cell culture system or the liver stem cell media described herein. In some embodiments, the kit further comprises reagents for isolating hepatocytes from a liver, such as a collagenase digestion solution.

In another aspect, a method of obtaining and/or culturing a liver stem cell is described, the method comprising: culturing primary cells obtained from a liver in the cell culture system described herein; the medium described herein, or using the components of a kit described herein. In some embodiments, the liver stem cell is obtained from a human liver. In some embodiments, the liver stem cell is a non-differentiated (pluripotent) cell.

Also provided are isolated liver stem cells obtained from the methods described herein.

In another aspect, a method of generating differentiated cells is described, the method comprising: growing a liver stem in a cell culture system capable of differentiating the liver stem cell into a plurality of differentiated cells.

In another aspect, a cell culture system for differentiating a liver stem cell into a hepatocyte is provided, the cell culture system comprising:

-   -   a) a plurality of soluble components comprising:         -   at least one Notch inhibitor;         -   at least one TGF-beta inhibitor; and     -   b) conditions for inducing epithelial cell polarization of the a         liver stem cell.

In some embodiments, the conditions for inducing epithelial cell polarization of the liver stem cell comprise culturing the liver stem cell at an air-liquid interface (ALI). When culturing the cell at the ALI, the basal side of the liver stem cell is configured to be in contact with the soluble components of the cell culture system and the apical surface of the liver stem cell is configured to be in contact with air.

In some embodiments, the plurality of soluble components further comprises at least one growth factor suitable for differentiating a liver stem cell into a hepatocyte. In some embodiments, the growth factor is selected from an IL6-like cytokine, oncostatin M, or LIF. In some cases, the concentration of the growth factor in the system is from about 5 ng/ml to about 200 ng/ml, or about 10 ng/ml to about 100 ng/ml, or about 15 ng/ml to about 70 ng/ml, or about 20 ng/ml to about 50 ng/ml, or about 16 ng/ml, or about 17 ng/ml, or about 18 ng/ml, or about 19 ng/ml, or about 20 ng/ml, or about 21 ng/ml, or about 22 ng/ml, or about 23 ng/ml, or about 24 ng/ml, or about 25 ng/ml.

In some embodiments, the TGF-beta inhibitor is 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), LY 364947 (4-[3-(2-pyridinyl)-1H-pyrazol-4-yl]-quinoline, or HTS 466284), SD 208 (2-(5-Chloro-2-fluorophenyl)pteridin-4-yl]pyridin-4-yl-amine), D4476 (4-(4-(2,3-Dihydrobenzo[1,4]dioxin-6-yl)-5-pyridin-2-yl-1H-imidazol-2-yl)benzamide), GW 788388 (4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide), SB 505124 (2-(5-Benzo[1,3]dioxol-5-yl-2-tert-butyl-3H-imidazol-4-yl)-6-methylpyridine), SB 525334 (6-[2-tert-Butyl-5-(6-methyl-pyridin-2-yl)-1H-imidazol-4-yl]-quinoxaline), RepSox (E-616452; or 2-[3-(6-Methyl-2-pyridinyl)-1H-pyrazol-4-yl]-1,5-naphthyridine), R 268712 (4-[2-Fluoro-5-[3-(6-methyl-2-pyridinyl)-1H-pyrazol-4-yl]phenyl]-1H-pyrazole-1-ethanol) or 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide (SB 431542). In some embodiments, the concentration of TGF-beta inhibitor in the system is from about 0.1 μM to about 5 μM, or about 0.1 μM to about 2.5 μM, or about 0.1 μM to about or about 0.1 μM, or about 0.2 μM, or about 0.3 μM, or about 0.4 μM, or about 0.5 μM, or about 0.6 μM, or about 0.7 μM, or about 0.8 μM, or about 0.9 μM.

In some embodiments, the plurality of soluble component further comprises at least one steroid. In some cases, the steroid is selected from the group consisting of dexamethasone, betamethasone, cortisone, methylprednisolone, prednisolone, prednisone, triamcinolone, and hydrocortisone. In some embodiments, the concentration of steroid in the system is from about 1 μM to about 100 μM, or about 10 μM to about 75 μM, or about 20 μM to about 50 μM, or about 20 μM, or about 25 μM, or about 30 μM, or about 35 μM, or about 35 μM, or about 40 μM, or about 45 μM.

In some cases, the system comprises at least one Notch inhibitor. The Notch inhibitor can be selected from the group consisting of N2-[(2S)-2-(3,5-Difluorophenyl)-2-hydroxyethanoyl]-N1-[(7S)-5-methyl-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl]-L-alaninamide (Ly411575), gamma-secretase inhibitor XXI (or compound E (N-[(1S)-2-[[(3S)-2,3-Dihydro-1-methyl-2-oxo-5-phenyl-1H-1,4-benzodiazepin-3-yl]amino]-1-methyl-2-oxoethyl]-3,5-difluorobenzeneacetamide)), FLI-06 (1,4,5,6,7,8-Hexahydro-2,7,7-trimethyl-4-(4-nitrophenyl)-5-oxo-3-quinolinecarboxylic acid cyclohexyl ester), RO4929097 (Propanediamide; or N1-[(7S)-6,7-dihydro-6-oxo-5H-dibenz[b,d]azepin-7-yl]-2,2-dimethyl-N3-(2,2,3,3,3-pentafluoropropyl)-malonamide), LY450139 ((2S)-2-hydroxy-3-methyl-N-((1S)-1-methyl-2-{[(1S)-3-methyl-2-oxo-2,3,4,5-tetrahydro-1H-3-benzazepin-1-yl]amino}-2-oxoethyl)butanamide), YO-01027 (7-(S)-[N′(3,5-difluorophenylacetyl)-L-alaninyl]amino-5-methyl-5,7-dihydro-6H-dibenz[b,d]azepin-6-one), BMS-708163 ((2R)-2-(N-(2-fluoro-4-(1,2,4-oxadiazol-3-yl)benzyl)-4-chlorophenylsulfonamido)-5,5,5-trifluoropentanamide), and BMS-906024 ((2R,3S)—N-[(3S)-1-Methyl-2-oxo-5-phenyl-2,3-dihydro-1H-1,4-benzodiazepin-3-yl]-2,3-bis(3,3,3-trifluoropropyl)succinamide). In some embodiments, the concentration of Notch inhibitor in the system is from about 0.05 μM to about 0.3 μM, or about 0.05 μM to about 0.2 μM, or about 0.05 μM to about 0.1 μM, or about 0.10 or about 0.15 μM.

In some embodiments, the system further comprises at least one Yes-associated protein (YAP) inhibitor. In some embodiments, the YAP inhibitor is selected from the group consisting of verteporfin (3-[(23 S,24R)-14-ethenyl-5-(3-methoxy-3-oxopropyl)-22,23-bis(methoxycarbonyl)-4,10,15,24-tetramethyl-25,26,27,28-tetraazahexacyclo[16.6.1.13,6.18,11.113,16.019,24]octacosa-1,3,5,7,9,11(27),12,14,16,18(25),19,21-dodecaen-9-yl]propanoic acid), ML7 (1-(5-Iodonaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine hydrochloride); blebbistatin (1-Phenyl-1,2,3,4-tetrahydro-4-hydroxypyrrolo[2.3-b]-7-methylquinolin-4-one), and Y27632 (trans-4-[(1R)-1-Aminoethyl]-N-4-pyridinylcyclohexanecarboxamide dihydrochloride). In some cases, the concentration of YAP inhibitor in the system is from about 0.1 μM to about or about 0.1 μM to about 0.7 μM, or about 0.1 μM to about 0.5 μM, or about 0.2 or about 0.3 or about 0.4 or about 0.5 or about 0.6 or about 0.7 or about 0.8 μM.

In some cases, the system further comprises a basal medium. In some embodiments, the basal medium is a liver specific basal medium hepatocyte culture medium, such as Clonetics™ HCM™ Hepatocyte Culture Medium.

In some embodiments, the system further comprises a cellular support capable of providing structural and nutritional support. In some embodiments, the cellular support comprises feeder cells. In some embodiments, the feeder cells are from a fibroblast cell line, such as a mouse or human fibroblast cell line. In some embodiments, the mouse fibroblast cell line is a 3T3J2 feeder cell line.

In some embodiments, the conditions for culturing the liver stem cell at the air-liquid interface (ALI) is achieved by a permeable cell culture apparatus, such as a Transwell® Permeable Support.

In another aspect, a cell culture system for differentiating a liver stem cell into a hepatocyte is provided. In some embodiments, the cell culture system for differentiating a liver stem cell into a hepatocyte comprises or consists of:

-   -   a plurality of soluble components comprising or consisting of:     -   a liver specific basal medium, A83-01, dexamethasone, oncostatin         M, compound E; IL6 and verteporfin;     -   conditions for culturing the liver stem cell at the air-liquid         interface (ALI),

In some embodiments, the basal side of the liver stem cell is configured to be in contact with the soluble components of the cell culture system and the apical surface of the liver stem cell is configured to be in contact with air.

In some embodiments, the hepatocyte is a fully differentiated mature hepatocyte. In some embodiments, the fully differentiated mature hepatocyte is characterized by at least one of the characteristics selected from the group consisting of:

-   -   a. functional CYP3A4 and CYP2C9 activity,     -   b. upon stimulation, the hepatocyte can uptake LDL, and/or         secrete albumin, and/or store glycogen,     -   c. expresses six CYP450 family member genes, and     -   d. does not express substantial amounts of AFP as compared to         fetal liver cells.

In another aspect, a kit comprising the components of the cell culture system for differentiating a liver stem cell into a hepatocyte is provided.

In another aspect, a method of differentiating a liver stem cell into a hepatocyte is described, the method comprising:

-   -   a. mixing the soluble components of the cell culture system or         the kit for differentiating a liver stem cell into a hepatocyte         with at least one liver stem cell;     -   b. culturing the liver stem cell in the soluble components until         confluency in cell population is obtained.

In some embodiments, after achieving confluency in cell population in step (b), the cells are cultured at the air-liquid interface (ALI), wherein the basal side of the liver stem cell is configured to be in contact with the soluble components of the cell culture system and the apical surface of the liver stem cell is configured to be in contact with air.

In another aspect, an isolated differentiated hepatocyte obtained from the methods described herein is provided.

In another aspect, a method of generating a plurality of differentiated liver cells is described, the method comprising: growing the liver stem cells described herein in a cell culture system capable of differentiating the cell into a plurality of differentiated liver cells.

In another aspect, a culture system for differentiating a liver stem cell into a biliary duct cell/cholangiocyte is provided. In some embodiments, the culture system is a substantially TGF-beta inhibitor and Notch inhibitor-free cell culture system. In some embodiments, the cell culture system comprises: an extracellular matrix for differentiating a liver stem cell into a 3D bile duct structure, and a liver stem cell described herein.

In some embodiments, the cell culture system further comprises at least one, at least two, at least three, or at least four growth factors suitable for differentiating a liver stem cell into a biliary duct cell. In some embodiments, the system comprises two, three or four growth factors suitable for differentiating a liver stem cell into a biliary duct cell. In some cases, the system comprises at least one growth factor selected from the group consisting of epidermal growth factor (EGF), fibroblast growth factor (FGF), TGF-beta, growth differentiation factor 11 (GDF11), a Notch pathway ligand, a Jag 1 protein having the amino acid sequence CDDYYYGFGCNKFCRPR; Jag 2; Delta-like protein 1 (DLL1); Delta-like protein 3 (DLL3), and Delta-like protein 4 (DLL4)). In some embodiments, the two growth factors are epidermal growth factor and fibroblast growth factor. In some embodiments, the fibroblast growth factor is selected from the group consisting of fibroblast growth factor 2 (FGF2) and fibroblast growth factor 10 (FGF10).

In some embodiments, the concentration of fibroblast growth factor in the system is from about 10 ng/ml to about 200 ng/ml, or about 30 ng/ml to about 150 ng/ml, or about 50 ng/ml to about 130 ng/ml, or about 60 ng/ml, or about 70 ng/ml, or about 80 ng/ml, or about 90 ng/ml, or about 100 ng/ml, or about 110 ng/ml, or about 120 ng/ml.

In some embodiments, the concentration of epidermal growth factor in the system is from about 5 ng/ml to about 100 ng/ml, or about 5 ng/ml to about 70 ng/ml, or about 5 ng/ml to about 50 ng/ml, or about 6 ng/ml, or about 7 ng/ml, or about 8 ng/ml, or about 9 ng/ml, or about 10 ng/ml, or about 11 ng/ml, or about 12 ng/ml, or about 13 ng/ml, or about 14 ng/ml, or about 15 ng/ml, or about 20 ng/ml, or about 25 ng/ml, or about 30 ng/ml, or about 35 ng/ml, or about 40 ng/ml, or about 45 ng/ml.

In some cases, the system is free of TGF-beta inhibitor and Notch inhibitor. In other words, the cell cultured system does not comprise a TGF-beta inhibitor or a Notch inhibitor.

In some embodiments, the biliary duct cell/cholangiocyte is a fully differentiated mature bile duct epithelial cell, which is characterized by at least one of the characteristics selected from the group consisting of:

-   -   a. cells having biliary duct-like 3 dimensional (3D) structure;     -   b. cells expressing KRT19 (Accession no: P08727.4) and KRT7         (Accession no: P08729.5) protein; and     -   c. cells having epithelial polarity.

In some embodiments, the liver stem cell that is differentiated into a biliary duct cell/cholangiocyte is a mammalian liver stem cell, such as a human liver stem cell, a mouse liver stem cell, or a fetal liver stem cell. In some cases, the liver stem cell is a liver stem cell obtained from a subject with liver disease selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

In some embodiments, the extracellular matrix is matrigel—such as a growth factor reduced matrigel.

In another aspect, a cell culture system for differentiating a liver stem cell into a biliary duct cell/cholangiocyte is provided, the cell culture system comprising an extracellular matrix, an epidermal growth factor and a fibroblast growth factor.

In another aspect, a kit comprising components of the cell culture system for differentiating a liver stem cell into a biliary duct cell/cholangiocyte described herein is provided.

In another aspect, a method of differentiating a liver stem cell into a biliary duct cell is described, the method comprising:

-   -   a. contacting components of the cell culture system for         differentiating a liver stem cell into a biliary duct cell, or         the components of the kit described herein with at least one         liver stem cell; and     -   b. culturing the liver stem cell in the components of the cell         culture system for at least one day to differentiate the liver         stem cell into a biliary duct cell.

In some embodiments, the culturing in step (b) is performed for at least two days, at least three days, at least four days, at least five days, at least six days, at least seven days, at least two weeks, or at least four weeks before the liver stem cell differentiates into a biliary duct cell.

In some embodiments, the components of the system or kit are provided or added to step (b) once every two days, or once every three days, or once every four days, or once every five days, or once every six days.

In another aspect, an isolated biliary duct cell/cholangiocyte obtained from the methods of differentiating a liver stem cell into a biliary duct cell/cholangiocytes is provided.

In another aspect, a hepatocyte differentiation medium is provided, the hepatocyte differentiation medium comprising or consisting of culture medium, 0.5 μM to 1 μM A83-01, 0.1 μM to 100 μM dexamethasone (Dex), and a γ-secretase inhibitor XXI/compound E or a Notch pathway inhibitor. In some embodiments, the concentration of dexamethasone is 0.1 μM, 0.5 μM, 1 μM, 5 μM, 10 μM, 20 μM, 30 μM 50 μM, or 100 μM. In some embodiments, the culture medium is selected from Clonetics™ HCM™ Hepatocyte Culture Medium, advanced DMEM/F12 (1:1) medium with B27 and N2, or DMEM/F12 (1:1) medium with 10% FBS. In some cases, the hepatocyte differentiation medium further comprises about 10 to 300 ng/ml BMP7, about 5 to 200 ng/ml FGF19, and/or about 1 to 200 ng/ml oncostatin M (OSM).

In some embodiments, the hepatocyte differentiation medium further comprises 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, or 300 ng/ml BMP7. In some embodiments, the hepatocyte differentiation medium further comprises 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, or 200 ng/ml FGF19. In some embodiments, the hepatocyte differentiation medium further comprises 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, or 200 ng/ml OSM.

In some embodiments, the concentration of the γ-secretase inhibitor XXI/compound E is between 0.1 nM and 100 nM, or about 0.1 μM.

In some embodiments, the Notch pathway inhibitor is DAPT (N—[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester) or Dibenzazepine (DBZ).

In another aspect, a cholangiocyte differentiation medium is provided, the cholangiocyte differentiation medium comprising or consisting of basal medium, 0.1% to 5% N2 (Gibco), 0.1% to 5% B27 (Gibco), 0.1 to 100 ng/ml EGF, and 5 to 200 ng/ml FGF10.

In the cell culture media embodiments described herein, the basal medium can be advanced F12/DMEM reduced serum medium. In some embodiments, the liver stem cell medium, hepatocyte differentiation medium, and/or cholangiocyte differentiation medium further comprise a buffer such as HEPES, an antibiotic such as Pen/Strep, and an amino acid such as L-Glutamine.

In another aspect, methods of treating a subject having liver disease are described. In some embodiments, the method comprises administering a liver stem cell described herein to the subject, such as by contacting the liver stem cell with the liver of the subject in vivo, or by transplanting a liver stem cell into the liver of the subject, wherein the administered or transplanted cell integrates into and repopulates the liver of the subject, thereby treating the liver disease. In some embodiments, the method comprises administering a differentiated liver stem cell described herein to the subject, such as by contacting the differentiated liver stem cell with the liver of the subject in vivo, or by transplanting a liver stem cell into the liver of the subject, wherein the administered or transplanted cell integrates into and repopulates the liver of the subject, thereby treating the liver disease. In some embodiments, the liver disease is selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, cirrhosis, and liver cancer.

Also provided are liver stem cells, and differentiated liver stem cells, described herein for use in the treatment of liver disease. Also provided are liver stem cells, and differentiated liver stem cells, described herein for use as a medicament in the treatment of liver disease. Also provided are the use of the liver stem cells, and differentiated liver stem cells, described herein for the manufacture of a medicament for the treatment of liver disease.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Liver stem cell isolation method. A). Protocol of liver stem cell isolation. B). Bright field images of each step of protocol.

FIG. 2: Isolation and derivation of adult human liver bipotent stem cell. Isolation and derivation of liver stem cell (LSC) from human liver tissue. Immunofluorescence staining (IF) of LSC derived from human liver tissue. LSC expressed stem cell marker Sox9, epithelial marker EPCAM and hepatocyte markers HNF4α and HNF3β. Bile duct marker Krt19 was lowly expressed. KRT7 and AFP were not detected. KRT7 is a cholangiocyte differentiation marker and Afp is expressed by immature hepatocytes. E-Cadherin (E-CAD), another epithelial cell marker, was also expressed in LSC. KI67 was homogenously expressed in LSC, indicating that all of the stem cells were proliferating. The figure shows that LSC is a near homogenous proliferating epithelial stem cell population (hepatocytes and cholangiocytes are of the epithelial lineage), and their marker expression is consistent with bipotent (hepatocyte and cholangiocyte) differentiation potential. KRT7 and KRT19 are bile duct markers. In previous reports, the cells strongly expressed KRT19 and KRT7, suggesting they are primed towards the bile duct lineage. The LSC express low levels of KRT19 and did not express KRT7, indicating they were not primed towards the bile duct lineage.

FIG. 3: Sporadic rare population of differentiated cells (bile duct lineage differentiation) express high level of KRT7 and KRT19, IF staining of LSC default differentiation with bile duct markers SRY (Sex Determining Region Y)-Box 9 (SOX9), KRT19 and KRT7. Undifferentiated LSC did not express KRT7 and low expression of KRT19, and rare sporadic differentiated LSC in the culture has strong expression of KRT7 and KRT19. The differentiated cells were irregular in shaped compared with undifferentiated LSC, which are round. They were flattened and were larger in size compared with undifferentiated LSC. The figure shows that differentiated cells were of bile duct lineage. KRT7 and KRT19 are not stem cell specific markers but are bile duct markers. In both prior art, their cells strongly expressed KRT19 and KRT7 suggesting they are primed towards the bile duct lineage.

FIG. 4: Human liver stem cell express liver stem cell markers. Microarray analysis of LSC, ESC (embryonic stem cell) and MRC5 human fibroblast. LSC were isolated from individual healthy donors and liver cirrhosis patients. All of LSC from different patients and donors express human liver stem cell markers SOX9, CD24 Molecule (CD24), EPCAM, Prominin 1 (PROM1), Forkhead Box A3 (FOXA3) and Forkhead Box Q1 (FOXQ1). Y-axis indicated the gene expression relative intensity.

FIGS. 5A and 5B: Human liver stem cell express low level of hepatocyte markers. FIG. 5A. Microarray hepatocyte gene expression heatmap of LSC, MRC5 human fibroblast and liver tissue. L1, L2 and L6 were individual healthy donors, CL1 and CL2 were liver cirrhosis patients. 2-6 cell lines from each patients were tested. LSC express low level of hepatocyte markers Albumin (ALB), Prospero Homeobox 1 (PROX1), HNF4α and Forkhead Box A2 (FOXA2), CYP2C9, 2E1 and 3A5. FIG. 5B. Quantitative polymerase chain reaction (qPCR) validation of hepatocyte gene expression in LSC and MRC5 fibroblast cell. This figure shows bipotent liver stem cells have hepatocyte gene signature but are distinct from differentiated liver cells.

FIG. 6: The same culture system is able to derive liver stem cells from mouse and human fetal tissue. Mouse liver tissue and human fetal liver tissue was digested with the same adult human liver digestion method. The digested cells was plated on feeder with LSC medium. Mouse and human fetal liver stem cell formed colonies with small clustered cells. Bright field images of the LSCs are shown. These cells expressed liver stem cell marker Sox9, Hnf4a and EpCam. This figure shows human fetal, mouse and potentially other mammalian species' liver stem cells could be derived using the methods described herein.

FIGS. 7A and 7B: LSC was derived from both Epcam+ and Epcam− liver cell population. A). Diagram of hepatic epithelial cell population classified by surface markers for cell sorting. Mouse liver epithelial cells were fluorescence-activated cell sorting (FACS) sorted by cell surface markers to separate cholangiocytes (EpCam+E-cad−) and hepatocytes (EpCam−E-cad+). B). Fluorescence-activated cell sorting (FACS) sorted cell populations were cultured with LSC media on feeder cells and were able to self-renew, as shown by the bright field images. Therefore LSC was derived from both Epcam+ cholangiocyte lineage and Epcam− hepatocyte lineage populations.

FIG. 8: LSC was derived from both healthy liver donor and liver disease patients. Brightfield images of LSC derived from liver diseased patients including HBV induced liver cirrhosis, alcoholic liver cirrhosis, hepatocarcinoma (HCC), Nonalcoholic Fatty Liver Disease (NAFLD) and Nonalcoholic Steatohepatitis (NASH). All of the LSC expressed liver stem cell markers: Epcam, SOX9, HNF4a, KRT19; HCC LSC expressed AFP and alb. Therefore LSC could be derived from both healthy and diseased livers.

FIG. 9: Long term culture of human liver epithelial stem/progenitor (LSC) cells. Bright view image of LSC on feeder cells. Both early passage 1 and late passage 16 have similar morphology. LSC are small round shape cells clustered together to form colony on feeder. The cells are symmetrical and not polarized. The edge of the clone raised up. This figure is consistent with LSC being stem cells with long term self-renewal ability.

FIG. 10: Long term cultured human liver epithelial stem/progenitor (LSC) cells have normal karyotype. Long term cultured human liver stem cells at passage 19 (280 days in culture) show normal karyotype. Left panel showed karyotyping results for 20 cells. All of the cells have normal karyotype. This figure shows that LSC maintained a stable genome during long term culture.

FIG. 11: Relationship between stem cell self-renewal and differentiation (or commitment). Stem cell self-renewal can occur in two ways: symmetric renewal and asymmetrical divisions. Stem cells go through symmetric renewal to expand the pool of stem cells, but they undergo asymmetric division to generate differentiated cells, and stem cells are present in a small proportion. Known liver organoids exhibit asymmetric division, and the organoid culture is a mixture of stem cells and differentiated bile duct cells. The 2D LSC culture goes through the symmetric renewal in that every stem cell was able to proliferate and maintained stem cell marker expression. This homogenous stem cells culture enables high efficiency differentiation to hepatocytes. Prior art cultures containing differentiated hepatocytes were always contaminated with a significant proportion of cholangiocytes. Furthermore, a pure stem cell population maintained in culture will increase the stem cell expansion efficiency.

FIG. 12: Minimal medium for LSC culture. Bright field images of LSCs grown in different media conditions for six passages. Full medium—Jagged1: cells keep growing in undifferentiated status. Full medium—CTX (cholera enterotoxin): cells grow faster than full medium but cells are loose (not so compact) and can be passaged. CTX not critical but help to maintain the cells in good undifferentiated quality. Full medium—T3: cells colony morphology changed. Cells trend towards differentiation but still could be passaged.

FIG. 13: Replacement of N2 and B27 with serum caused LSC differentiation. Bright view image of LSC culture in medium with 10% serum without B2 and N27, and control serum free medium with N2 and B27. We observed that the use of serum based media disclosed in WO2014152321 A1 did not maintain the liver cell morphology in an undifferentiated state.

FIG. 14: LSC derived on fibroblast feeders. Brightfield images of LSC cells were cultured on J2, L1, Swiss 3T3, NIH3T3 separately. J2 feeder cultured LSC formed the largest colony. L1 formed the smallest colony. We continued culturing for more than one year for J2, but did not test beyond that time frame. Swiss3T3, NIH3T3, L1 also could support LSC growing for at least 5 passages. We did not test longer than this timeframe.

FIG. 15: Feeder-free culture of LSC. Feeder-free culture of LSC in J2 conditional medium. Culture condition: Collagen I &IV and Laminin 521, 511 coated plate with feeder conditional medium. Result: LSC could be cultured for at least 5 passages in feeder-free 2D culture by J2 conditional medium.

FIGS. 16A and 16B: Differentiation of LSC. FIG. 16A. LSC has self-renewal ability and bilineage differentiation potential. It is able to differentiate into both hepatocytes and bile duct cells. FIG. 16B. 3D bile duct cell (cholangiocytes) differentiation: 30000-50000 LSC cells was seeded in one well of an 8-chamber slide. The well was previously coated with 60 μl of matrigel. The matrigel form a dome shape in the well. LSC aggregated on the surface of matrigel to form a sphere structure. The sphere structures grew bigger and bigger in culture medium. When the medium was changed to bile duct differentiation medium, the sphere stopped growing and started bile duct differentiation. This figure shows the 3D bile duct differentiation model.

FIGS. 17A and 17B: LSC 2D hepatocytes differentiation. FIG. 17A. Diagram of LSC differentiate into hepatocyte in 2D culture model. FIG. 17B. LSC was cultured on feeder in culture dish until 100% confluence. The medium was changed into hepatocyte initiation medium for 3-5 days and then switched to hepatocyte differentiation medium for another 14 days. The differentiated cells expressed hepatocyte marker HNF4a, ALB, CYP2C9 and terminal differentiation marker Phosphoenolpyruvate Carboxykinase 1 (PEPCK). Tight junction marker Zona Occludens 1 (ZO1) was expressed between differentiated cells. This figure shows that LSC differentiated into hepatocyte in 2D culture with specific hepatocyte markers expression. The differentiated hepatocyte matured with terminal differentiation markers expression.

FIG. 18: High efficiency hepatocyte differentiation from LSC. High efficiency 2D hepatocyte differentiation. Differentiated cells were dissociate into single cells, fixed and stained with hepatocyte marker HNF4α (FITC) and ALB (Texas red). Stained cells were analyzed by fluorescence-activated cell sorting (FACS). Histogram showed 86% of cells were ALB+, and 92% of cells were HNF4α+. This figure shows that LSC hepatocyte differentiation were highly efficient and produced a high purity hepatocyte population.

FIG. 19: Quantitative albumin secretion assay of LSC differentiated hepatocyte. Human alubumin (hAlb) ELISA assay to quantitative analysis albumin secretion in culture medium. HepG2 cell line and embryonic stem cell H1 line (ESC(H1)) were used as negative control, ESC differentiated hepatocyte (eHep) was used as positive control. This figure shows that LSC differentiated hepatocyte (dHep) were functional with albumin secretion.

FIG. 20A: CYP activity of differentiated hepatocytes (dHep). A. LSC in vitro differentiated hepatocyte (dHep) Cytochrome P450 functions were tested by Promega P450-glo CYP450 Assay Kit. HepG2 cell line was used as positive control for comparison. Luciferin intensity were normalized by differentiated cell numbers. dHep had high CYP3A4, CYP2C9, CYP2B6 and CYP1A2 activities. It indicates the dHep were matured hepatocytes with matured hepatocyte function.

FIG. 20B: Drug induced CYP activity of differentiated hepatocytes. Drug induced CYP functions were tested by Promega P450-glo CYP450 Assay Kit. CYP3A4 and CYP2C9 were induced for 48 hrs with 10 μM rifampicin (RIF). Luciferin intensity were normalized by differentiated cell numbers. This figure shows that dHep were matured hepatocytes that respond to drug induction.

FIG. 21: Major CYP p450 family members have detectable RNA expression. qPCR analysis of LSC in vitro differentiated hepatocyte (dHep). Mature hepatocyte specific genes expression of differentiated LSC were compared with undifferentiated LSC. Fold change is as indicated by the y-axis. This figure shows that dHep expressed major CYPs. That indicated dHep were mature hepatocytes.

FIG. 22: ICG uptake and release assay of LSC 2D differentiated dHep. ICG (cardiogreen) uptake and release by dHep. 1 mg/ml ICG were incubated with dHep at 37° C. for 1 hour for uptake function test. Image was taken under bright view. Cells which uptook ICG were blue. After 1 hour of incubation, cells were washed and incubated with culture medium. Culture medium were harvest at 1, 2, 3 hour separately and tested by spectrometer at 820 nM. ICG were release into the culture medium by differentiated cell at 3 hours. This figure shows that dHep had ion transport function similar to primary hepatocytes.

FIG. 23: Lipid uptake assay and glycogen storage capability of LSPC 2D differentiated hepatocyte. Periodic acid Schiff (PAS) staining and low-density lipoprotein (LDL) uptake assay. PAS staining was carried on 2D differentiated hepatocyte. Ubiquitous staining of glycogen stored in dHep cytosol (left panel). LDL uptake assay was shown in middle and left panels. dHep was incubated with fluorescently-labeled LDL at 37° C. for 1 hour. Cells that uptake LDL were stained red. This figure shows that dHep had lipid uptake function similar to primary hepatocytes.

FIG. 24: 3D hepatocyte differentiation in suspension culture. LSC were dissociated from culture dish and cultured in 96 plate in hepatocyte initiation medium for 7 days and switched to hepatocyte differentiation medium for another 14 days. Cells aggregated and formed a spheroid. The hepatocyte 3D spheroids were fixed and stained with hepatocyte marker ALB (red) and bile duct marker KRT7 (green). Almost 100% of cells differentiated into hepatocytes (ALB+KRT7−). This figure shows almost 100% differentiation of LSC into hepatocytes.

FIG. 25: LSC differentiated hepatocyte (dHep) expressed ALB. The dHep cells were around 100% ALB+. Terminal differentiation marker PEPCK1 and Tyrosine Aminotransferase (TAT) were also expressed.

FIG. 26: LSC differentiated into hepatocytes in air liquid interface (ALI) culture. IF staining of hepatocyte markers on LSC differentiated hepatocyte by ALI. LSC differentiated cells had terminal differentiated hepatocyte markers ALB, PEPCK and TAT expression. They also expressed drug metabolism enzyme CYP p450 family proteins CYP2C9. Key hepatocyte transcription factor Hnf4a was expressed in cell nucleus. dHep also have tight junctions, as indicated by ZO1. This figure shows LSC differentiated into mature hepatocyte in ALI culture.

FIG. 27: 3D differentiated cholangiocytes cultured on matrigel formed organoids with bile duct structure. Bright view image of organoids with bile-duct-like structures. Majority of the organoids are spheriodal in structure with columnar shaped epithelial cells. Liquid can be observed in the spheres suggesting that the cholangiocytes are secreting mucus.

FIG. 28: Differentiated cholangiocytes are 100% positive for bile duct epithelial cell markers KRT19 and KRT7. Cryosections of 3D bile duct structures were stained with bile duct marker KRT19 and KRT7. The cells are columnar shape and well organized. They strongly express bile duct marker KRT7 and KRT19. They were well polarized. Their nucleus located in the bottom part near basal membrane (matrigel side). In the luminal part microvilli are formed. This figure showed terminally differentiated bile duct cells. This is the first report of terminally differentiated bile duct cells in vitro.

FIGS. 29A and 29B: LSC differentiated into bile duct cells in 3D culture. FIG. 29A). Bright view of bile duct-like structure. FIG. 29B). IF staining of bile duct markers on organoid sections. Cholangiocytes expressed KRT19 and KRT7, which are bile duct lineage markers. The columnar bile duct cells were well organized with the differentiated cholangiocyes being fully polarized with microvilli on the luminal apical part of the cells; nucleus near the basal membrane. Tight junction marker ZO-1 expressed in cell junction.

FIGS. 30A and 30B: Liver stem cell derived from liver disease subjects have altered gene expression reflective of their disease phenotype. FIG. 30A). RNA-seq data analysis of LSC from NAFLD subjects, Hepatitis B virus (HBV) infected liver cirrhosis subjects and healthy liver donors. Two individual patient samples from each disease and a healthy control group. Principle component analysis (PCA) plot showed LSC from different disease groups are clustered within the disease group, indicating that LSC from subjects with the same disease have similar altered gene expression patterns. FIG. 30B). Gene enrichment analysis (GSEA) shows NAFLD stem cells enriched of fatty acid biosynthesis, amino acid metabolism imbalance and insulin pathway down regulation compared with healthy and HBV infected cirrhosis liver stem cells. This shows that NASH LSC keep NASH related phenotypes.

FIG. 31: Single cell derived HCC stem cells form tumor in mouse liver. LSC from a hepatocellular carcinoma (HCC) patient were derived from a single cell culture. These HCC LSCs expressed AFP, in contrast with LSC derived from healthy donors. HCC LSC were transplanted into NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mouse strains, which are immunodeficient. Transplanted HCC LSCs developed into tumors in mouse liver of both mouse 1 & mouse 2 (photographs with tumors circled with large circle). H&E staining showed undifferentiated HCC from tumor regions compared with normal histology from normal tissue. This figure showed single cell derived HCC LSC are able to form tumors.

FIGS. 32A and 32B: Human albumin-expressing HCC cells were present in tumor mass and infiltrated adjacent mouse liver tissue. FIG. 32A). Human specific albumin IHC staining in mouse liver. Human albumin (hALB) was expressed in both tumor mass formed by transplanted HCC LSC. hALB was also expressed in mouse liver tissue adjacent to the tumor mass. Arrows indicate hALB staining. FIG. 32B). Human ALB (hALB) ELISA in mouse serum. HCC LSC transplanted mouse had hALB in its serum. This figure shows that the tumor were derived from transplanted HCC LSC which differentiated into albumin secreting cells in mouse liver.

FIGS. 33A and 33B: Rescued liver function on LSC transplanted TA induced liver cirrhosis mice model. FIG. 33A). Schematic of transplantation into TA liver cirrhosis mice model for liver regeneration. Thioacetamide (TA) was metabolized in adult mouse hepatocytes and produce toxic metabolite that damage the hepatocytes to induce liver cirrhosis. FIG. 33B). TA liver cirrhosis mice model showed that liver function was rescued in LSC transplanted mice. Transplanted mice blood serum ALB levels were significantly higher than control group which did not have LSC transplantation.

FIG. 34: LSC differentiated into human Alb positive hepatocyte when transplanted into mouse liver. Human ALB immunohistochemistry (IHC) staining on mouse liver, human liver and mouse liver with transplanted LSC. LSC transplanted into mouse liver tissue were detected by staining with hALB-specific antibody in IHC. This figure showed LSC differentiate into functional ALB-expressing hepatocyte in mouse liver.

FIG. 35: Gross view of LSC differentiated hepatocyte transplanted mice liver. Gross view of LSC differentiated hepatocyte (dHep) transplanted mice liver. dHep were transplanted into TA induced liver cirrhosis mice. Control group had 3 mice without dHep transplantation. Transplanted group had 6 mice. This figure shows that dHep transplanted livers were rescued from liver cirrhosis as judged by liver morphology. The control cirrhotic liver with no cell transplanted have multiple cirrhotic nodules on the surface of the liver. In contrast, the liver with transplanted hepatocytes have a smooth surface similar to normal healthy liver.

FIG. 36: dHep repopulated mouse liver in TA liver cirrhosis model. Livers from control and dHep transplanted livers in TA liver cirrhosis model were stained for hALB using a hALB-specific antibody. hALB staining was detected only in dHep transplanted mouse livers demonstrating repopulation of mouse liver by dHep.

FIG. 37: Isolation and derivation of adult mouse liver stem cell (LSC). Immunofluorescence staining (IF) of LSC derived from mouse liver tissue. LSC expressed stem cell marker epithelial marker Epcam and hepatocyte marker Hnf4α. Bile duct marker Krt19 was lowly expressed and Krt7 was not detected. E-cad, an epithelial cell marker was also expressed in LSC. The figure shows that isolated and derived LSC is a homogenous epithelial stem cell population.

DEFINITIONS

The term “about,” when modifying any amount, refers to the variation in that amount typically encountered by one of skill in the art, i.e., in the field of liver stem cell derivation and differentiation. For example, the term “about” refers to the normal variation encountered in measurements for a given analytical technique, both within and between batches or samples. Thus, the term about can include variation of 1-10% of the measured amount or value, such as +/−1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% or 10% variation. The amounts disclosed herein include equivalents to those amounts, including amounts modified or not modified by the term “about.”

All numerical ranges disclosed herein include the lower and upper end points of the range, and all numerical values in between the end points, to the significant digit. For example, a range of 1 to 10 includes 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10. A range of 0.1 to 5.0 includes 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, . . . 4.8, 4.9, and 5.0.

The term “growth factor reduced” matrigel refers to a matrigel in which growth factors were partially removed. The term includes Corning® Matrigel® Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning cat. #356230), which comprises a matrix comprising a solubilized basement membrane preparation extracted from the Engelbreth-Holm-Swarm (EHS) mouse sarcoma, a tumor rich in extracellular matrix proteins, including Laminin (a major component), Collagen IV, heparin sulfate proteoglycans, entactin/nidogen, and a number of growth factors.

The term “substantially” when referring to expression of a gene, protein or cellular marker refers to the complete or nearly complete extent or degree of expression. For example, a cell population that is “substantially” negative of a particular cellular marker is either completely negative for the particular cellular marker or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.9% of the cell population is negative for the particular cellular marker. A cell culture system that is “substantially” free of a particular agent would mean that the cell culture system is either completely free of the agent or is at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.9% free of the particular agent.

The term “extracellular matrix” refers to natural or artificial cellular-free scaffolding for cell growth. In some embodiments, natural extracellular matrix is a complex mixture of structural and non-structural biomolecules, including but not limited to, collagens, elastins, laminins, glycosaminoglycans, proteoglycans, antimicrobials, chemoattractants, cytokines and growth factors. In one example, the extracellular matrix is a gelatinous protein mixture secreted by mouse sarcoma cells (such as Engelberth-Holm-Swarm (EHS)) cells.

The term “undetectable” refers to the absence of, or not more than 2-fold greater detectable marker expression when compared to background expression or expression by a negative control. For example, if the assay is an immunofluorescence (IF) staining assay, then expression is considered “undetectable” if the fluorescent signal is not greater than 2-fold the background signal when omitting the primary detection antibody, or has similar fluorescence staining to a control cell that does not express the marker (i.e., is negative for the marker). If the assay is a microarray assay, then expression of the marker is considered “undetectable” if the relative intensity is less than 2-fold higher than a negative control sample.

The term “low levels” refers to marker expression that is at least 2-fold, but not more that 5-fold greater than the background expression or expression by a negative control. For example, if the assay is an immunofluorescence (IF) staining assay, then expression is considered “low levels” if the fluorescent signal is at least 2-fold and not more than 5-fold greater than the background signal when omitting the primary detection antibody, or is at least 2-fold and not more than 5-fold greater than the fluorescence signal of a control cell that does not express the marker (i.e. is negative for the marker). In IF staining, low level of expression also means the fluorescent intensity is more than 2-fold lower than a positive control sample (e.g., a bile duct lineage differentiated cell). In microarray assays, low level of expression also means the RNA expression is at least 2-fold lower than a positive control sample (e.g., bile duct lineage differentiated cells).

DETAILED DESCRIPTION OF THE INVENTION

The present inventors have developed methods for producing liver stem cells (LSC) that can be used to produce mature, differentiated hepatocytes and cholangiocytes in culture. The inventors have developed cell culture systems that produce a homogenous population of liver stem cells that maintain the ability to proliferate in culture and remain in an undifferentiated state over multiple passages, which was confirmed by the expression of stem cell markers during extended culture. The methods and cells described herein provide the unexpected advantage of providing a source of liver stem cells that can be used to produce differentiated mature hepatocytes and cholangiocytes at high frequency.

Stem cell self-renewal and differentiation is tightly linked. Stem cells self-renew in two ways, symmetric renewal and asymmetrical divisions (FIG. 11). Symmetrical self-renewal enables stem cells to expand in numbers while during asymmetric division, differentiated cells are generated and stem cells are kept in a relatively small population. The hepatic stem cells described herein underwent symmetric self-renewal; every stem cell was able to proliferate and maintain stem cell marker expression. This homogenous stem cell culture provides the advantage of high efficiency in deriving hepatocytes and cholangiocytes. The homogeneity of stem cell culture also increases the stem cell expansion efficacy as fewer cells are lost through differentiation during maintenance or sub-culturing steps.

The ability to generate homogenous liver stem cell cultures enables efficient high-throughput generation of homogenous hepatocytes and cholangiocytes for downstream applications. When liver stem cell populations are non-homogenous, the differentiation process results in a mixture of immature and mature hepatocytes and cholangiocytes. This mixture of cells would result in deviations and erroneous observations in applications. For example in the assessment of drug induced toxicity, the drug may target only mature hepatocytes in the dish and remaining cells remain viable. This results in erroneous conclusions regarding drug toxicity. On the other hand, the compound may be affecting the immature cells and cholangiocytes instead of the mature hepatocytes. When the starting culture is non-homogenous, the proportion of cells varies in each set of differentiation, thus resulting in inconsistency between each set of experiments. This will be detrimental for assays such as in vitro toxicity which requires high standardization between each runs. Large amount of cells would be needed for in vivo transplantation. A heterogeneous stem cell culture will only generate small amount of target cells. It will be a challenging task to generate sufficient cells for transplantation without a homogenous starting population of stem cells.

The liver stem cells (LSC) described herein include the following desirable characteristics:

-   -   (i) the stem cells are bipotential and maintained their         undifferentiated and bipotential state during long term culture;     -   (ii) the stem cells can be differentiated in vitro into mature         bile duct cells (cholangiocytes) expressing the ductal markers         KRT7 and KRT19, polarized columnar cell phenotype, typical         tubular structure, and cilia on the luminal surface of the         cells;     -   (iii) the stem cells can be differentiated in vitro into mature         functional hepatocytes by 2D, 3D and air-liquid interface (ALI)         differentiation methods;     -   (iv) the differentiated hepatocytes (dHEP) were functional based         on several different phenotypes, including glucose and lipid         metabolism, and CYP function (four different CYP enzymes);     -   (v) the stem cells were generated from both healthy donor and         liver disease patients, and the stem cells from diseased         patients maintained the liver disease phenotype;     -   (vi) the stem cells differentiated into functional (albumin         secreting) hepatocytes in vivo when transplanted into mouse         liver using a in vivo model of liver cirrhosis (the chemical         induced liver mouse model); and     -   (vii) stem cells differentiated in vitro into hepatocytes were         able to repopulate injured mouse liver and execute hepatocyte         functions.

Specific embodiments will now be described.

Liver Stem Cell Culture System

The liver stem cell culture system described herein comprises a plurality of soluble agents in a stem cell culture media and a cellular support capable of providing structural and nutritional support. The cellular support maintains the liver stem cells in a monolayer adhesion, thus preventing the formation of 3D structures such as spheroids or organoids. The cellular support provides both structural support and cytokines that plays a part in maintaining liver stem cells in the undifferentiated state. In some embodiments, the cellular support maintains the liver stem cells in a 2D structure (such as a monolayer). In some embodiments, the plurality of soluble agents comprises one or more growth factors, an enhancer of the (canonical) WNT pathway, and a stem cell differentiation inhibitor.

The liver stem cell culture system described herein comprises a liver stem cell culture media having one or more of the following ingredients: a stem cell differentiation inhibitor (e.g., a TGF-beta signaling inhibitor), a WNT agonist, thyroid hormone(s), a growth factor, and Nicotinamide. In some embodiments, the liver stem cell culture system comprises a liver stem cell culture media having or consisting of all of the following ingredients: a stem cell differentiation inhibitor (e.g., a TGF-beta signaling inhibitor), a WNT agonist, thyroid hormone(s), a growth factor, and Nicotinamide. In some embodiments, the liver stem cell culture system comprises a liver stem cell culture media having or consisting of all of the following ingredients: a stem cell differentiation inhibitor (e.g., a TGF-beta signaling inhibitor), a WNT agonist, cholera enterotoxin, a growth factor, and Nicotinamide.

In some embodiments, the stem cell differentiation inhibitor is a TGF-beta signaling inhibitor. For example, the TGF-beta inhibitor can block activation of TGF-beta pathway, which induces stem cell differentiation, whereas inactivation of the TGF-beta pathway maintains liver stem cells during long term culture. In some embodiments, the TGF-beta inhibitor is selected from the group consisting of A83-01 (3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide) and SB431542 (4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide). In some embodiments, the concentration of SB431542 in the cell culture system is between about 0.1 ng/ml and about 10 ng/ml, e.g., from about 0.1 ng/ml to about 10 ng/ml, or about 0.5 ng/ml to about 8 ng/ml, or about 2 ng/ml to about 7 ng/ml, or about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

The enhancer of the canonical WNT pathway stimulates liver stem cell proliferation. In the absence of the enhancer of the canonical WNT pathway, the liver stem cells may undesirably differentiate into matured liver cells. In some embodiments, the enhancer of the canonical WNT pathway is a WNT agonist. In some embodiments, the WNT agonist is selected from the group consisting of a Wnt family member (Wnt-1/Int-1, Wnt-2/Irp (Int-1-related Protein), Wnt-2b/13, Wnt-3/Int-4, Wnt-3a, Wnt-4, Wnt-5a, Wnt-5b, Wnt-6, Wnt-7a, Wnt-7b, Wnt-8a/8d, Wnt-8b, Wnt-9a/14, Wnt-9b/14b/15, Wnt-10a, Wnt-10b/12, Wnt-11, and Wnt-16); an R-spondin family member (R-spondin 1, R-spondin 2, R-spondin 3, and R-spondin 4), Norrin (Norrie Disease Protein or NDP), and Norrin (Norrie Disease Protein or NDP), a Glycogen synthase kinase 3 inhibitor selected from small-interfering RNAs, lithium, kenpaullone, 6-Bromoindirubin-30-acetoxime, SB 216763 (3-(2,4-Dichlorophenyl)-4-(1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione), SB 415286 (4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide; CHIR 99021 (6-[[2-[[4-(2,4-Dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2-pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile), CHIR 99021 trihydrochloride (6-[[2-[[4-(2,4-Dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2-pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile trihydrochloride), Kenpaullone, Indirubin-3′-oxime, MeBIO ((2′Z,3′E)-6-Bromo-1-methylindirubin-3′-oxime) TCS 2002 (2-Methyl-5-[3-[4-(methylsulfinyl)phenyl]-5-benzofuranyl]-1,3,4-oxadiazole), Lithium carbonate, NSC 693868 (1H-Pyrazolo[3,4-b]quinoxalin-3-amine), TCS 21311(3-[5-[4-(2-Hydroxy-2-methyl-1-oxopropyl)-1-piperazinyl]-2-(trifluoromethyl)phenyl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione), AR-A 014418 (N-[(4-Methoxyphenyl)methyl]-N′-(5-nitro-2-thiazolyl)urea), 3F8 (5-Ethyl-7,8-dimethoxy-1H-pyrrolo[3,4-c]isoquinoline-1,3(2H)-dione), L803 (Peptide KEAPPAPPQSP), A 1070722 (1-(7-Methoxyquinolin-4-yl)-3-[6-(trifluoromethyl)pyridin-2-yl]urea), 10Z-Hymenialdisine, TC-G 24 (N-(3-Chloro-4-methylphenyl)-5-(4-nitrophenyl)-1,3,4-oxadiazol-2-amine), TWS 119 3-[[6-(3-Aminophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]oxyphenol ditrifluoroacetate]), and L803-mts (peptide GKEAPPAPPQSP); a FRAT-family member (FRAT: frequently rearranged in advanced T-cell lymphomas) and FRAT-derived peptides. In some embodiments, the Wnt agonist is R-spondin. In certain embodiments, the concentration of R-spondin in the stem cell culture medium is between about 25 and about 500 ng/ml, e.g., about 25, 50, 100, 125, 250, or 500 ng/ml. In some embodiments, the concentration of R-spondin 1 in the stem cell culture system is between about 25 and about 500 ng/ml, or about 100 ng/ml to about 500 ng/ml, or about 110 ng/ml to about 400 ng/ml, or about 150 ng/ml to about 350 ng/ml, or about 200 ng/ml to about 300 ng/ml, or about 230 ng/ml to about 270 ng/ml, or about 25 ng/ml, or about 50 ng/ml, or about 100 ng/ml, or about 125 ng/ml, or about 235 ng/ml, or about 240 ng/ml, or about 245 ng/ml, or about 250 ng/ml, or about 255 ng/ml, or about 260 ng/ml, or about 265 ng/ml, or about 500 ng/ml.

In some embodiments, the growth factor is Epidermal Growth Factor (EGF) and/or thyroid hormone. In some embodiments, the growth factor is EGF. In some embodiments, the concentration of Epidermal Growth Factor (EGF) in the stem cell culture medium was between about 5 ng/ml and about 200 ng/ml, e.g., from about 5 ng/ml to about 200 ng/ml, or about 10 ng/ml to about 150 ng/ml, or about 35 ng/ml to about 100 ng/ml, or about 40 ng/ml to about 60 ng/ml, or about 41 ng/ml, or about 42 ng/ml, or about 43 ng/ml, or about 44 ng/ml, or about 45 ng/ml, or about 46 ng/ml, or about 47 ng/ml, or about 48 ng/ml, or about 49 ng/ml, or about 50 ng/ml, or about 51 ng/ml, or about 52 ng/ml, or about 53 ng/ml, or about 54 ng/ml, or about 55 ng/ml, or about 56 ng/ml, or about 57 ng/ml, or about 58 ng/ml, or about 59 ng/ml.

In some embodiments, the growth factor is thyroid hormone. In some embodiments, the thyroid hormone is selected from the group consisting of 3,3′-5-triiodo-1-thyronine (T3), (5)-thyroxine (T4), and hormones that stimulate cAMP, such as parathyroid hormone (PTH), the adenosine A2 receptor agonist 5′-(N-ethylcarboxamido)-adenosine (NECA), prostaglandin E2, or forskolin. In some embodiments, the thyroid hormone is T3. In some embodiments, the concentration of T3 in the cell culture system is between about 0.2 μM and about 20 μM, e.g., from about 0.2 μM to about 20 μM, or about 0.1 μM to about 15 μM, or about 1 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM, or about 10 μM, or about 11 μM, or about 12 μM, or about 13 μM, or about 14 μM.

In some embodiments, the concentration of Nicotinamide in the stem cell culture system is between about 1 mM and about 50 mM, e.g., from about 1 mM to about 50 mM, or about 1 mM to about 25 mM, or about 5 mM to about 15 mM, or about 6 mM, or about 7 mM, or about 8 mM, or about 9 mM, or about 10 mM, or about 11 mM, or about 12 mM, or about 13 mM, or about 14 mM.

In some embodiments, the liver stem cell culture media can also optionally include Cholera enterotoxin (also called Cholera endotoxin) (CTX). Cholera toxin was added in the culture to minimize presence of differentiated cells. In some embodiments, the concentration of Cholera endotoxin in the media was between about 0.01 μM and about 1 μM, e.g., from about 0.01 μM to about 1 μM, or about 0.05 μM to about 0.9 μM, or about 0.95 μM, or about 0.05 μM, or about 0.1 μM, or about 0.2 μM, or about 0.3 μM, or about 0.4 μM, or about 0.5 μM, or about 0.6 μM, or about 0.7 μM, or about 0.8 μM, or about 0.9 μM. Higher concentrations (>0.1 μM) of cholera endotoxin inhibited cell proliferation rather than stimulating growth. As shown in FIG. 12, CTX is not required, but helps maintain the stem cells in an undifferentiated state. In some embodiments, CTX can replace thyroid hormone (such as T3) as an agent that can stimulate the cell to release cAMP and increase the cell's metabolic rate.

In some embodiments, the liver stem cell culture media is a serum-free media. Adding 2%, 5%, 8%, 10%, 15% and 20% fetal bovine serum (FBS) and withdrawing B27 and N2 from the culture medium simulated stem cell differentiation. The differentiated cells expressed higher Krt7 and Krt19 than undifferentiated stem cells, but lower or no HNF4α expression. Thus, including B27 and N2 in the medium helped to maintain the stem cells in the undifferentiated status, but FBS failed to do so and instead stimulated stem cell differentiation (FIG. 13).

Bone Morphogenetic Protein (BMP) antagonists have been reported to be essential for liver epithelial stem cell culture (see WO2014152321 A1). However, the culture medium does not require an antagonist or inhibitor of BMP. Thus, in some embodiments, the culture system does not comprise an antagonist or inhibitor of BMP. For example, the BMP antagonist Noggin was not added to the culture medium.

In some embodiments, the culture system does not comprise HGF (Hepatocyte Growth Factor), and/or FGF (Fibroblast Growth Factor).

In certain embodiments, N-Acetyl-Cysteine (NAC) was added in the culture medium to attenuate reactive-oxygen-species-mediated stress in cell culture. It helped to maintain the liver stem cell in undifferentiated status especially in long term culture. In some embodiments, the concentration of N-acetyl-cysteine in the cell culture media is between about 0.1 μM and about 10 μM, for example, from about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In certain embodiments, an agent for activating the Notch pathway was optionally added to the culture medium to stimulate cell proliferation. In some embodiments, the agent for activating the Notch pathway is a Notch ligand. In some embodiments, the Notch ligand is Jagged-1. In some embodiments, Jagged-1 has the amino acid sequence CDDYYYGFGCNKFCRPR (SEQ ID NO:1). In some embodiments, 0.1, 0.5, 1, 5, 10 μM Jagged-1 was added in the culture medium to stimulate the cell proliferation. In some embodiments, the concentration of Jagged-1 in the culture medium is between about 0.1 μM to about 10 μM, or about 1 μM to about 10 μM, or about 0.1 μM, or about 0.5 μM, or about 1.0 μM, or about 2 μM, or about 3 μM, or about 4 μM, or about 5 μM, or about 6 μM, or about 7 μM, or about 8 μM, or about 9 μM.

In some embodiments, the liver stem cell culture medium comprises or consists of about 0.1% to about 5% N2, about 0.1% to about 5% B27, between about 5 ng/ml and about 200 ng/ml EGF, between about 25 and about 500 ng/ml R-Spondin 1, between about 0.1 μM and about 10 μM SB431542 (4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide), between about 0.1 μM to about 10 μM T3 (3,3′,5-Triiodo-L-Thyronine), and between about 1 mM and about 50 mM Nicotinamide. In some embodiments, the liver stem cell culture medium further comprises a basal medium such as advanced F12/DMEM reduced serum medium, a buffer such as HEPES (e.g., about 1 to about 50 mM HEPES), an antibiotic such as about 10 to about 200 U/ml Pen/Strep, and an amino acid, such as about 0.5 to about 5 mM L-Glutamine.

In one embodiment, the liver stem cell culture medium comprises or consists of Advanced F12/DMEM reduced serum medium (1:1) (Gibco. 12643), 10 mM HEPES (Gibco), 100U/ml Pen/Strep (Gibco), 2 mM L-Glutamine (Gibco), 1% N2 (Gibco), 2% B27 (Gibco), 50 ng/ml EGF (Millipore), 250 ng/ml R-Spondin1 (R&D), 2 μM SB431542 (Tocris)), 2 μM T3 (3,3′,5-Triiodo-L-Thyronine)(Sigma), and 10 mM Nicotinamide (Sigma).

In some embodiments, mouse fibroblasts were used as feeder cells in the liver stem cell culture. Mouse fibroblasts used as feeder cells for liver stem cell cultures included 3T3J2, Swiss3T3, NIH3T3 and L1 cells. However, it is understood that cells from other organisms, e.g., fibroblast cells from other mammals, can be used as feeder cells. For example, human fibroblast cells can be used as feeder cells.

In certain embodiments, 1%, 2%, 5%, or 10% Matrigel was used to coat the culture dish before thawing the cryopreserved fibroblast cells. Matrigel was diluted with advanced F12/DMEM basal medium. 10% Matrigel supplied nutrition to the fibroblast feeder cells and helped the fragile irradiated feeder cells to attach firmly to the culture plate, so that the feeder cells could be used for at least 2 weeks to support the stem cells. This coating step is optional, since early passage (<10 passage) J2 was able to support the stem cell without Matrigel coating.

In certain embodiments, fibroblast feeder density lower than 0.5×10⁶ cells per 10 cm culture plate failed to maintain the stem cells in undifferentiated status. The fibroblast feeder provides both attachment support and secretes growth factors and cytokines that sustain the hepatic stem cell state. Thus, low density of feeders may result in insufficient growth factors to support stem cell growth.

In certain embodiments, liver stem cells were maintained using feeder-cell free cultures. In some embodiments, the liver stem cells were cultured on an extracellular matrix comprising a mixture of Collagen I/Collagen IV, and Laminin 511/Laminin 521 without feeder cells in feeder-cell conditioned medium. As shown in FIG. 15, the feeder-free culture could be used to maintain the liver stem cells in an undifferentiated state for up to 5 passages. In some embodiments, the extracellular matrix does not induce stem cell differentiation. For example, the extracellular matrix can be a growth factor free (such as TGF-beta free) or growth factor reduced matrix, such that it does not stimulate stem cell differentiation.

Liver Stem Cells

Liver stem cells described herein could be generated from both hepatocyte and non-hepatocyte liver populations in the liver. The human hepatic stem cells express adult stem cell marker SOX9 and hepatocyte markers HNF4α and HNF3β (FIG. 2). The undifferentiated stem cells expressed low levels of Bile duct marker KRT19 (Accession no: P08727.4), but did not express detectable levels of bile duct marker KRT7 (Accession no: P08729.5) (protein expression level as determined by immunofluorescence staining). The hepatic stem cells also expressed other liver stem cell markers EPCAM, CD24, PROM1, FOXA3 and FOXQ1 (FIG. 2, FIG. 4). Morphologically, undifferentiated stem cells were small, round in shape and clustered tightly together. The hepatic stem cells were not polarized (FIG. 8). Almost all the cells in culture were proliferating as all the cells expressed Ki67 in the cell nucleus (FIG. 2). The hepatic stem cells described herein differ from naturally occurring stem cells. For example, naturally occurring stem cells have not been reported to express the FOXA3 and FOXQ1 markers.

In some embodiments, the liver stem cell described herein comprises the following characteristics:

-   -   (i) expresses at least 1, 2, 3 or 4 of the protein markers         selected from SOX9, HNF4α, HNF3β, and EPCAM;     -   (ii) expresses low levels of KRT19 protein,     -   (iii) does not express detectable protein levels of KRT7 or AFP;         and     -   (iv) does not have a polarized cell phenotype.

In some embodiments, the liver stem cell further expresses 1, 2, 3, 4, or 5 protein markers selected from CD24, PROM1, FOXA3, FOXQ1 and ECAD. The characteristics of the stem cell are maintained in long-term culture, and comprise a normal karyotype after 19 passages in culture.

The liver stem cell can be derived from a mammal, such that the liver stem cell can be a mammalian liver stem cell, a human liver stem cell, a mouse liver stem cell, or a fetal liver stem cell. In some embodiments, the liver stem cell is isolated from a healthy subject. In some embodiments, the liver stem cell is isolated from a subject with liver disease, wherein the liver disease is selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

As shown in FIG. 5A, human liver stem cells express low levels of hepatocyte markers Albumin (ALB), Prospero Homeobox 1 (PROX1), HNF4α and Forkhead Box A2 (FOXA2), CYP2C9, CYP 2E1 and CYP 3A5. As shown in FIG. 5B, qPCR validation of hepatocyte gene expression in LSC and MRC5 fibroblast cells shows that the bipotent liver stem cells have a hepatocyte gene signature but are distinct from differentiated liver cells.

During the maintenance of stem cells, colonies of differentiated cells were also observed. The differentiated liver cells showed strong levels of ECAD, KRT19, KRT7 expression and decreased expression of SOX9 (FIG. 3), consistent with the differentiated cells being ductal in nature. Sporadic differentiated cells were larger and flatter in shape (FIG. 3).

Mouse liver stem cells were also isolated using the methods described herein. As shown in FIG. 37, mouse liver stem cell expressed EPCAM and HNF4a, low levels of KRT19, but did not express detectable levels of KRT7.

The liver stem cells form disk like clones and push the non-soluble support (such as feeder cells) to the side. In one example, where the cellular support is provided under high density conditions (such as feeder cells at >2×10⁶ cells per 10 cm plate), the liver stem cells form dome shape clones, not spheres. In some embodiments, the liver stem cells form several wrinkle structures inside the clone in the early passage of cells when they were just derived from liver tissue. In some embodiments, the early passage is the first passage after isolation from liver tissue. “Early passage” refers to passage 0, or passage 0 to 1, or passage 0 to 2, or passage 0 to 3, or passage 0 to 4, where passage 0 is the first passage after isolation from liver tissue and before the isolated liver cells are cultured. The wrinkle structures typically disappear after continuing culture for several passages.

In contrast, the liver stem cells previously described in the art are:

-   -   a. 100% positive of KRT19,     -   b. around 50% KRT7 positive,     -   c. E-CAD positive, EPCAM positive, SOX9 positive, and KRT7         positive,     -   d. Less than about 70-100%, or less than about 100%, or less         than about 90% or less than 80% positive for the transcription         factor for hepatocyte lineage differentiation such as HNF4a,     -   e. cultured as organoids with a mixture of partially         differentiated bile duct cells and hepatocyte progenitor/stem         cells; and     -   f. when differentiated into hepatocytes, only have one         functional CYP enzyme (CYP3A4).

Cell Culture System and Methods for Producing Differentiated Hepatocytes

Cell culture systems and methods for producing differentiated hepatocytes from liver stem cells are described herein. In some embodiments, the cell culture system comprises a plurality of soluble components comprising: at least one Notch inhibitor; at least one TGF-beta inhibitor; and conditions for inducing epithelial cell polarization of the liver stem cell. In some embodiments, the conditions for inducing epithelial cell polarization of the liver stem cell comprise culturing the liver stem cell at the air-liquid interface (ALI), Such that the basal side of the liver stem cell is in contact with the soluble components of the cell culture system and the apical surface of the liver stem cell is in contact with air.

In some embodiments, the plurality of soluble components further comprises at least one growth factor suitable for differentiating a liver stem cell into a hepatocyte. In some embodiments, the growth factor is selected from an IL6-like cytokine, including oncostatin M and LIF.

In some embodiments, the concentration of the growth factor in the system is from about 5 ng/ml to about 200 ng/ml, or about 10 ng/ml to about 100 ng/ml, or about 15 ng/ml to about 70 ng/ml, or about 20 ng/ml to about 50 ng/ml, or about 16 ng/ml, or about 17 ng/ml, or about 18 ng/ml, or about 19 ng/ml, or about 20 ng/ml, or about 21 ng/ml, or about 22 ng/ml, or about 23 ng/ml, or about 24 ng/ml, or about 25 ng/ml.

In some embodiments, the TGF-beta inhibitor is 3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide (A83-01), LY 364947 (4-[3-(2-pyridinyl)-1H-pyrazol-4-yl]-quinoline, or HTS 466284), SD 208 (2-(5-Chloro-2-fluorophenyl)pteridin-4-yl]pyridin-4-yl-amine), D4476 (4-(4-(2,3-Dihydrobenzo[1,4]dioxin-6-yl)-5-pyridin-2-yl-1H-imidazol-2-yl)benzamide), GW 788388 (4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide), SB 505124 (2-(5-Benzo[1,3]dioxol-5-yl-2-tert-butyl-3H-imidazol-4-yl)-6-methylpyridine), SB 525334 (6-[2-tert-Butyl-5-(6-methyl-pyridin-2-yl)-1H-imidazol-4-yl]-quinoxaline), RepSox (E-616452; or 2-[3-(6-Methyl-2-pyridinyl)-1H-pyrazol-4-yl]-1,5-naphthyridine), R 268712 (4-[2-Fluoro-5-[3-(6-methyl-2-pyridinyl)-1H-pyrazol-4-yl]phenyl]-1H-pyrazole-1-ethanol) or 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide (SB 431542). In some embodiments, the concentration of TGF-beta inhibitor in the system is about 0.1 μM to about 5 or about 0.1 μM to about 2.5 μM, or about 0.1 μM to about 1 or about 0.1 μM, or about 0.2 μM, or about 0.3 μM, or about 0.4 μM, or about 0.5 μM, or about 0.6 μM, or about 0.7 μM, or about 0.8 μM, or about 0.9 μM.

The plurality of soluble components can further comprise at least one steroid. In some embodiments, the steroid is selected from the group consisting of dexamethasone, betamethasone, cortisone, methylprednisolone, prednisolone, prednisone, triamcinolone, and hydrocortisone. In some embodiments, the concentration of the steroid in the system is about 1 μM to about 100 or about 10 μM to about 75 or about 20 μM to about 50 or about 20 or about 25 or about 30 or about 35 or about 35 or about 40 or about 45 μM.

The system can also comprise at least one Notch inhibitor. In some embodiments, the at least one Notch inhibitor is selected from the group consisting of N2-[(2S)-2-(3,5-Difluorophenyl)-2-hydroxyethanoyl]-N1-[(7S)-5-methyl-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl]-L-alaninamide (Ly411575), gamma-secretase inhibitor XXI (or compound E (N-[(1S)-2-[[(3S)-2,3-Dihydro-1-methyl-2-oxo-5-phenyl-1H-1,4-benzodiazepin-3-yl]amino]-1-methyl-2-oxoethyl]-3,5-difluorobenzeneacetamide)), FLI-06 (1,4,5,6,7,8-Hexahydro-2,7,7-trimethyl-4-(4-nitrophenyl)-5-oxo-3-quinolinecarboxylic acid cyclohexyl ester), RO4929097 (Propanediamide; or N1-[(7S)-6,7-dihydro-6-oxo-5H-dibenz[b,d]azepin-7-yl]-2,2-dimethyl-N3-(2,2,3,3,3-pentafluoropropyl)-malonamide), LY450139 ((2S)-2-hydroxy-3-methyl-N-((1 S)-1-methyl-2-{[(1 S)-3-methyl-2-oxo-2,3,4,5-tetrahydro-1H-3-benzazepin-1-yl]amino}-2-oxoethyl)butanamide), YO-01027 (7-(S)-[N′(3,5-difluorophenylacetyl)-L-alaninyl]amino-5-methyl-5,7-dihydro-6H-dibenz[b,d]azepin-6-one), BMS-708163 ((2R)-2-(N-(2-fluoro-4-(1,2,4-oxadiazol-3-yl)benzyl)-4-chlorophenylsulfonamido)-5,5,5-trifluoropentanamide), and BMS-906024 ((2R,3S)—N-[(3S)-1-Methyl-2-oxo-5-phenyl-2,3-dihydro-1H-1,4-benzodiazepin-3-yl]-2,3-bis(3,3,3-trifluoropropyl)succinamide). In some embodiments, the concentration of Notch inhibitor in the system is from about 0.05 μM to about 0.3 or about 0.05 μM to about 0.2 μM, or about 0.05 μM to about 0.1 μM, or about 0.10 or about 0.15 μM.

In some embodiments, the system further comprises at least one Yes-associated protein (YAP) inhibitor. The YAP inhibitor can be selected from the group consisting of verteporfin (3-[(23 S,24R)-14-ethenyl-5-(3-methoxy-3-oxopropyl)-22,23-bis(methoxycarbonyl)-4,10,15,24-tetramethyl-25,26,27,28-tetraazahexacyclo[16.6.1.13,6.18,11.113,16.019,24]octacosa-1,3,5,7,9,11(27),12,14,16,18(25),19,21-dodecaen-9-yl]propanoic acid), ML7 (1-(5-Iodonaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine hydrochloride); blebbistatin (1-Phenyl-1,2,3,4-tetrahydro-4-hydroxypyrrolo[2.3-b]-7-methylquinolin-4-one), and Y27632 (trans-4-[(1R)-1-Aminoethyl]-N-4-pyridinylcyclohexanecarboxamide dihydrochloride). In some embodiments, the concentration of YAP inhibitor in the system is from about 0.1 μM to about or about 0.1 μM to about 0.7 μM, or about 0.1 μM to about 0.5 μM, or about 0.2 μM, or about 0.3 μM, or about 0.4 μM, or about 0.5 μM, or about 0.6 μM, or about 0.7 μM, or about 0.8 μM.

In some embodiments, the system further comprises a basal medium. The basal medium can be a liver specific basal medium hepatocyte culture medium, such as Clonetics™ HCM™ Hepatocyte Culture Medium.

In some embodiments, the system further comprises a cellular support capable of providing structural and nutritional support. In some embodiments, the cellular support comprises feeder cells. In some embodiments, the feeder cells are from a fibroblast cell line, such as a mouse or human fibroblast cell line. In some embodiments, the mouse fibroblast cell line is a 3T3J2 feeder cell line.

In some embodiments, the conditions for culturing the liver stem cell at the air-liquid interface (ALI) is achieved by a permeable cell culture apparatus, such as a Transwell® Permeable Support.

In some embodiments, the cell culture system for differentiating a liver stem cell into a hepatocyte comprises or consists of:

-   -   a plurality of soluble components comprising or consisting of:     -   a liver specific basal medium, A83-01, dexamethasone, oncostatin         M, compound E; IL6 and verteporfin;     -   conditions for culturing the liver stem cell at the air-liquid         interface (ALI),

In some embodiments, the basal side of the liver stem cell is configured to be in contact with the soluble components of the cell culture system and the apical surface of the liver stem cell is configured to be in contact with air.

In some embodiments, the hepatocyte is a fully differentiated mature hepatocyte. In some embodiments, the fully differentiated mature hepatocyte is characterized by at least one of the characteristics selected from the group consisting of:

-   -   a. functional CYP3A4 and CYP2C9 activity,     -   b. upon stimulation, the hepatocyte can uptake LDL, and/or         secrete albumin, and/or store glycogen,     -   c. expresses six CYP450 family member genes, and     -   d. does not express substantial amounts of AFP as compared to         fetal liver cells.

Also provided are kits comprising the components of the cell culture system for differentiating a liver stem cell into a hepatocyte.

In some embodiments, the method of differentiating a liver stem cell into a hepatocyte comprises:

-   -   a. mixing the soluble components of the cell culture system or         the kit for differentiating a liver stem cell into a hepatocyte         with at least one liver stem cell;     -   b. culturing the liver stem cell in the soluble components until         confluency in cell population is obtained.

In some embodiments, after achieving confluency in cell population in step (b), the cells are cultured at the air-liquid interface (ALI), wherein the basal side of the liver stem cell is configured to be in contact with the soluble components of the cell culture system and the apical surface of the liver stem cell is configured to be in contact with air.

Also provided are methods of generating a plurality of differentiated liver cells, the method comprising: growing the liver stem cells described herein in a cell culture system capable of differentiating the cell into a plurality of differentiated liver cells.

Differentiated Hepatocytes

The differentiated hepatocytes described herein are characterized by expression of hepatocyte markers HNF4α, ALB, CYP2C9, and can also express the terminal differentiation marker PEPCK1. The tight junction marker ZO1 was expressed between differentiated cells. The differentiated hepatocytes also expressed functional CYP enzymes, including CYP3A4, CYP2C9, CYP2B6, CYP1A2, CYP1A1, CYP2D6, CYP3A7, and CYP2E1. The differentiated hepatocytes exhibited other features of mature hepatocytes, including functional glucose metabolism (determined by PAS staining for glycogen synthesis and storage), functional lipid metabolism (determined by low-density lipoprotein (LDL) uptake assay) (FIG. 23), indocyanine green (ICG) uptake (FIG. 22), and albumin secretion (FIG. 19). ICG uptake is a medical diagnostic test used for diagnosis of hepatic functions, and is used demonstrates that hepatocytes have functional transporter functions to transport ions in and out of the hepatocytes.

The hepatocytes presented here exhibit metabolic functions of the major CYPs, CYP1A2, CYP3A4, CYP2B6 and CYP2C9 (FIGS. 20A and 20B), which accounts for majority of compound metabolism activities of the liver. The expression and activity of other CYPs presented here suggest we can detect metabolic activity for all compounds that can be process by the liver. More importantly, the hepatocytes are shown to be responsive to known CYP inducing drugs such as Rifampicin.

In some embodiments, the differentiated hepatocyte comprises at least one of the following characteristics:

-   -   (i) expresses the markers HNF4α and ALB;     -   (ii) expresses at least 1, 2, 3, 4, 5, 6, 7 or 8 of the CYP         enzymes selected from CYP3A4, CYP2C9, CYP2B6, CYP1A2, CYP1A1,         CYP2D6, CYP3A7, and CYP2E1;     -   (iii) have at least 1, 2 or 3 of the following functions:         -   a) functional glucose metabolism;         -   b) functional lipid metabolism;         -   c) functional albumin secretion;     -   (vi) indocyanine green (ICG) uptake; and     -   (vii) forms tight junctions when cultured with other         differentiated hepatocytes under conditions sufficient to form         an epithelium.

The differentiated hepatocyte can also express at least one of the terminal differentiation markers PEPCK1 or TAT. The differentiated hepatocyte has inducible CYP function for at least 2, 3, or 4 of the CYPs selected from CYP3A4, CYP2C9, CYP2B6, CYP1A2, CYP1A1, CYP2D6, CYP3A7, and CYP2E1. The differentiated hepatocyte can also store glycogen and uptake low density lipoprotein.

In some embodiments, the differentiated hepatocyte is differentiated from a liver stem cell isolated from a healthy human or from a human with liver disease selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

Cell Culture System and Methods for Producing Differentiated Cholangiocytes

In some embodiments, methods and culture systems for producing differentiated cholangiocytes are described herein. In some embodiments, a culture system for differentiating a liver stem cell into a biliary duct cell/cholangiocyte is provided. In some embodiments, the culture system is a substantially TGF-beta inhibitor and Notch inhibitor-free cell culture system. In some embodiments, the cell culture system comprises: an extracellular matrix for differentiating a liver stem cell into a 3D bile duct structure, and a liver stem cell described herein.

In some embodiments, the cell culture system further comprises at least one, at least two, at least three, or at least four growth factors suitable for differentiating a liver stem cell into a biliary duct cell. In some embodiments, the system comprises two, three or four growth factors suitable for differentiating a liver stem cell into a biliary duct cell. In some cases, the system comprises at least one growth factor selected from the group consisting of epidermal growth factor (EGF), fibroblast growth factor (FGF), TGF-beta, growth differentiation factor 11 (GDF11), a Notch pathway ligand, a Jag 1 protein having the amino acid sequence CDDYYYGFGCNKFCRPR; Jag 2; Delta-like protein 1 (DLL1); Delta-like protein 3 (DLL3), and Delta-like protein 4 (DLL4)). In some embodiments, the two growth factors are epidermal growth factor and fibroblast growth factor. In some embodiments, the fibroblast growth factor is selected from the group consisting of fibroblast growth factor 2 (FGF2) and fibroblast growth factor 10 (FGF10).

In some embodiments, the concentration of fibroblast growth factor in the system is from about 10 ng/ml to about 200 ng/ml, or about 30 ng/ml to about 150 ng/ml, or about 50 ng/ml to about 130 ng/ml, or about 60 ng/ml, or about 70 ng/ml, or about 80 ng/ml, or about 90 ng/ml, or about 100 ng/ml, or about 110 ng/ml, or about 120 ng/ml.

In some embodiments, the concentration of epidermal growth factor in the system is from about 5 ng/ml to about 100 ng/ml, or about 5 ng/ml to about 70 ng/ml, or about 5 ng/ml to about 50 ng/ml, or about 6 ng/ml, or about 7 ng/ml, or about 8 ng/ml, or about 9 ng/ml, or about 10 ng/ml, or about 11 ng/ml, or about 12 ng/ml, or about 13 ng/ml, or about 14 ng/ml, or about 15 ng/ml, or about 20 ng/ml, or about 25 ng/ml, or about 30 ng/ml, or about 35 ng/ml, or about 40 ng/ml, or about 45 ng/ml.

In some cases, the system is free of TGF-beta inhibitor and Notch inhibitor. In other words, the cell cultured system does not comprise a TGF-beta inhibitor or a Notch inhibitor.

In some embodiments, the biliary duct cell/cholangiocyte is a fully differentiated mature bile duct epithelial cell, which is characterized by at least one of the characteristics selected from the group consisting of:

-   -   a. cells having biliary duct-like 3 dimensional (3D) structure;     -   b. cells expressing KRT19 (Accession no: P08727.4) and KRT7         (Accession no: P08729.5) protein; and     -   c. cells having epithelial polarity.

In some embodiments, the liver stem cell that is differentiated into a biliary duct cell/cholangiocyte is a mammalian liver stem cell, such as a human liver stem cell, a mouse liver stem cell, or a fetal liver stem cell. In some cases, the liver stem cell is a liver stem cell obtained from a subject with liver disease selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

In some embodiments, the extracellular matrix is matrigel—such as a growth factor reduced matrigel.

In some embodiments, the cell culture system comprises an extracellular matrix, an epidermal growth factor and a fibroblast growth factor.

Also provided are kits comprising components of the cell culture system for differentiating a liver stem cell into a biliary duct cell/cholangiocyte described herein.

In some embodiments, methods for differentiating a liver stem cell into a biliary duct cell are described, the method comprising:

-   -   a. contacting components of the cell culture system for         differentiating a liver stem cell into a biliary duct cell, or         the components of the kit described herein with at least one         liver stem cell; and     -   b. culturing the liver stem cell in the components of the cell         culture system for at least one day to differentiate the liver         stem cell into a biliary duct cell.

In some embodiments, the culturing in step (b) is performed for at least two days, at least three days, at least four days, at least five days, at least six days, at least seven days, at least two weeks, or at least four weeks before the liver stem cell differentiates into a biliary duct cell.

In some embodiments, the components of the system or kit are provided or added to step (b) once every two days, or once every three days, or once every four days, or once every five days, or once every six days.

Differentiated Cholangiocytes

The biliary duct cells/cholangiocytes described herein are fully differentiated mature bile duct epithelial cells. In some embodiments, the differentiated cholangiocytes are characterized by at least one of the characteristics below:

-   -   (i) expresses the markers KRT19 (Accession no: P08727.4) and         KRT7 (Accession no: P08729.5) and ECAD;     -   (ii) has columnar epithelial cell polarity comprising an apical         region and a basolateral region when cultured with other         differentiated cholangiocytes under conditions sufficient to         form an epithelium;     -   (iii) comprises microvilli on the apical region;     -   (iii) forms biliary duct-like 3 dimensional (3D) structure when         cultured with other differentiated cholangiocytes under         conditions sufficient to form 3D structures.

The differentiated cholangiocytes described herein have an asymmetrical organization that divides an individual cell unit into different regions such as an apical region and a basolateral region. The apical region is defined as the area lying above the tight junctions. The apical region may have microvilli structure on the luminal part of the 3D structure. The basolateral region is defined as the area below the tight junctions and contains the basolateral membrane which is in contact with basal lamina.

In some embodiments, the differentiated choloangiocyte is differentiated from a liver stem cell isolated from a healthy human or from a human with liver disease selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.

Kits

Also provided herein are kits comprising components of the cell culture systems or cell culture media described herein. In some embodiments, the kit comprises or consists of the components of the liver stem cell culture system or the liver stem cell media described herein. In some embodiments, the kit further comprises reagents for isolating hepatocytes from a liver, such as a collagenase digestion solution. In some embodiments, the kit comprises or consists of the components of the cell culture system for differentiating a liver stem cell into a hepatocyte. In some embodiments, the kit comprises or consists of components of the cell culture system for differentiating a liver stem cell into a biliary duct cell/cholangiocyte.

Methods of Treatment

In some embodiments, methods and pharmaceutical formulations for treating a subject having liver disease are provided. The subject can be a mammal suffering from liver disease. In some embodiments, the subject is a human suffering from liver disease or who otherwise could benefit from the methods described herein. In some embodiments, the method comprises administering a liver stem cell described herein to the subject, such as by contacting the liver stem cell with the liver of the subject in vivo, or by transplanting a liver stem cell into the liver of the subject, wherein the administered or transplanted cell integrates into and repopulates the liver of the subject, thereby treating the liver disease. In some embodiments, the method comprises administering a differentiated liver stem cell (dHEP) described herein to the subject, such as by contacting the differentiated liver stem cell with the liver of the subject in vivo, or by transplanting a liver stem cell into the liver of the subject, wherein the administered or transplanted cell integrates into and repopulates the liver of the subject, thereby treating the liver disease. In some embodiments, the liver disease is selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, cirrhosis, and liver cancer.

The liver stem cells and/or dHEP cells can be administered to a subject in the form of a pharmaceutical composition. The pharmaceutical composition can comprise a sterile isotonic excipient suitable for human administration. For general methods in pharmaceutical formulations, please see Cell Therapy: Stem Cell Transplantation, Gene Therapy, and Cellular Immunotherapy, by G. Morstyn & W. Sheridan eds, Cambridge University Press, 1996; and Hematopoietic Stem Cell Therapy, E. D. Ball, J. Lister & P. Law, Churchill Livingstone, 2000. The pharmaceutical composition comprising liver stem cells and/or dHEP cells can be administered based on the route and device used for administration. In some embodiments, the pharmaceutical composition comprises additional components that aid the engraftment of the cells in the liver of the subject. The liver stem cells or dHEP cells can be administered in an amount effective to treat or reduce the symptoms of liver disease in the subject. For example, about 1×10⁶, 2×10⁶, 3×10⁶, 4×10⁶, 5×10⁶ or more liver stem cells or dHEP cells can be administered in either a single dose or multiple doses.

EXAMPLES Example 1

Isolation and Long Term Culture of Human Liver Stem Cells

Materials & Methods:

Collagenase digestion Solution: DEME/F12 (Gibco) with 10 mM Hepes, 5% FBS (Clonetech), 2 mg/ml collagenase (Sigma, C-5138). Warm collagenase solution to 37 degree C., filter sterilize after the collagenase has gone into solution through a 0.2 micron filter. Make this media fresh (collagenase will inactivate at high temperatures and over long periods of time).

Washing solution: DEME/F12 medium with 10 mM HEPES (Gibco), 100U/ml Pen/Strep (Gibco), 100 μg/ml gentamicin (Gibco), filter sterilize solution through a 0.2 micron filter.

Coating medium: Growth factor reduced matrigel (Corning) 10%, diluted advanced F12/DMEM reduced serum medium (Gibco).

Liver stem cell culture medium: Advanced F12/DMEM reduced serum medium (1:1)(Gibco. 12643), 10 mM HEPES (Gibco), 100 U/ml Pen/Strep (Gibco), 2 mM L-Glutamine (Gibco), 1% N2 (Gibco), 2% B27 (Gibco), 50 ng/ml EGF (Millipore), 250 ng/ml R-Spondin1 (R&D), 2 μM SB431542 (Tocris)), 1 μM Jagged-1(188-204) (Anaspec), 2 μM T3 (3,3′,5-Triiodo-L-Thyronine)(Sigma), 0.1 μM Cholera endotoxin (Sigma), 10 mM Nicotinamide (Sigma), 1.25 μM N-Acetyl-Cysteine (NAC)(Sigma).

Preparation of Feeder Cell:

1. The plates were coated with 10% matrigel. Matrigel was diluted with advanced F12/DMEM basal medium. After coating the plates, the plates were store in 37° C. incubator for 30 min.

2. Vials containing 7×10⁶ cells/vial were thawed into 3 six well plates with 2 mL medium each well. The cells were thawed quickly in the waterbath, and swabbed with 70% alcohol before bringing them into a laminar-flow hood. The cells were added into a 50 mL tube and warm medium was added drop by drop to dilute the cells. 3. Shake the plates in the incubator (left and right ×2 & back and front ×2) to evenly distribute the cells 4. The feeder could be used on the second day.

Liver stem cells were isolated from fresh human liver tissue (FIG. 1). The use of human liver samples for hepatocyte preparation for scientific purposes were approved by Institutional Review Boards (IRBs) and Human Research Ethics committee. Normal liver samples were obtained from donor livers for transplantation. Cirrhosis liver samples were obtained from recipient liver for transplantation. The tissues was cut and minced into small pieces and digested in collagenase solution. The digested cells were suspended in liver stem cell culture medium. The cells were pooled and plated on tissue culture plates with feeder cells and allowed to attach. After 7-10 days, cells were harvested and resuspended as single cells and plated onto the feeders. Hepatic stem cell colonies start to appear 3 days later. The cells were subcultured every 7 to 10 days for long term culture. Culture medium was changed every 2 days.

Single cell derived cell lines were generated by picking up single colonies on feeder for continual culture. Early passaged liver stem cell was digested in single cells and retrieved by flow cytometry. The sorted single cell was cultured in 96 well plate and further split into 48, 24 and 6 wells plates for expansion.

In certain embodiments, the digested early passage cells were filtered through a 40 μm strainer and plated at a low density on the culture dish. After 10 to 14 days, single cells grew to form colonies without merging with other colonies. The single cell derived colonies were picked for continuing culture on 24 well plates. 1%, 10%, 20%, 30%, 40% and 50% of the cells repopulated in the next passaging.

Single cell derived hepatic stem cell line was passaged continuously every 7 to 14 days, early passage and late passage were checked for karyotyping. Cells at both passages have normal karyotype. This shows that the stem cell genomes were stable during long term culture (FIG. 9, FIG. 10).

Results:

The hepatic stem cells express adult stem cell marker SOX9 and hepatocyte markers HNF4α and HNF3β (FIG. 2). Bile duct marker KRT19 is lowly expressed and bile duct marker KRT7 is undetectable in the cells (protein level). The hepatic stem cell also expressed other liver stem cell marker EPCAM, CD24, PROM1, FOXA3 and FOXQ 1 (FIG. 2, FIG. 4). During the maintenance of stem cells, colonies of differentiated cells were observed (˜1-2% of total number of colonies). The differentiated liver cells showed strong levels of ECAD, KRT19, KRT7 expression and decreased express SOX9 (FIG. 3), consistent with the differentiated cells being ductal in nature. Morphologically, undifferentiated cells were small, round in shape and clustered tightly together. The hepatic stem cells were not polarized (FIG. 8). Sporadic differentiated cells were larger and flatter in shape (FIG. 3). Almost all the cells in culture were proliferating as all the cells expressed KI67 in the cell nucleus (FIG. 2). Morphologically, all of them were small round shape. The undifferentiated cells expressed low levels of KRT19, but did not express detectable levels of KRT7.

Example 2

Isolation and Long Term Culture of Mouse Liver Stem Cells

Liver stem cells described herein could be generated from both hepatocyte and non-hepatocyte liver populations in the liver. Mouse liver was digested into single cell suspension and labeled with bile duct marker EPCAM and the epithelial marker E-CAD. Cells of bile duct origin were EPCAM-positive and E-CAD-negative. Cells of hepatocyte origin were EPCAM-negative and E-cad-positive. Both bile duct and hepatocytes were isolated using FACS sorting and separately cultured using the methods described in the Examples. Liver stem cells were generated from both two cell populations (FIG. 7).

Liver stem cell culture medium was composed of Advanced F12/DMEM reduced serum medium (1:1)(Gibco. 12643), 10 mM HEPES (Gibco), 100U/ml Pen/Strep (Gibco), 2 mM L-Glutamine (Gibco), 1% N2 (Gibco), 2% B27 (Gibco), 50 ng/ml EGF (Millipore), 250 ng/ml R-Spondin1 (R&D), 2 μM SB431542 (Tocris)), 2 μM T3 (3,3′,5-Triiodo-L-Thyronine) (Sigma), 10 mM Nicotinamide (Sigma).

Jagged-1 (0.1, 0.5, 1, 5, 10 μM) was optionally added to the culture medium to stimulate the cell proliferation (FIG. 12).

Cholera endotoxin (0.05, 0.1 μM) was optionally added in the culture to minimize presence of differentiated cells. Higher concentrations (>0.1 μM) of cholera endotoxin inhibited cell proliferation rather than stimulating growth. However, the use of cholera endotoxin was not required to keep the stem cells in an undifferentiated state optional in the culture medium (FIG. 12).

N-Acetyl-Cysteine (1.25 μM) was added in the culture medium to attenuate reactive-oxygen-species-mediated stress in cell culture. It helped to maintain the liver stem cell in undifferentiated status especially in long term culture.

Mouse fibroblasts were used as feeders in liver stem cell culture. The fibroblast cells were cultured in DMEM medium with high glucose, 10% bovine calf serum, 100U/ml Pen/Strep and 2 mM L-Glutamine. Cells were grown to 70-80% confluence and irradiated with 6000 Rads. Mouse fibroblast used for liver stem cells including 3T3J2, Swiss3T3, NIH3T3 and L1.

Various concentrations of Matrigel (1%, 2%, 5%, 10%) was used to coat the culture dish before thawing the cryopreserved fibroblast cells. Matrigel was diluted with advanced F12/DMEM basal medium. After coating the plate, they were put in 37° C. incubator for 30 min. 10% Matrigel supplied nutrition to the fibroblast feeder and helped the irradiated fragile feeder to attach firmly to the culture plate, so that the feeder could be used for at least 2 weeks to support the stem cells. This coating step is optional, since early passage (<10 passage) J2 was able to support the stem cell without Matrigel coating.

Example 3

Differentiation of Liver Stem Cells to Hepatocytes

Liver Stem cells were able to differentiate into both hepatocyte and bile duct cell at near 100% efficiency. Hepatocyte differentiation were conducted in both 2D (FIG. 17), 3D (FIG. 24) and air liquid interface (ALI) format (FIG. 26). Bile duct differentiation was in 3D format (FIGS. 16A and 16B).

Hepatocyte differentiation medium consisted of Clonetics™ HCM™ Hepatocyte Culture Medium (Lonza) supplemented with 0.5 μM A83-01 (Tocris), 30 μM dexamethasone (Dex) (Sigma), 20 ng/ml oncostatin M (OSM) (Prospecbio), 0.1 μM γ-secretase inhibitor XXI, also called compound E (Santa cruz), 25 ng/ml Bmp7 and 25 ng/ml Fgf19.

In certain embodiments, Clonetics™ HCM™ Hepatocyte Culture Medium (Lonza) could be replaced with advanced DMEM/F12 (1:1) medium with B27, N2 or DMEM/F12 (1:1) medium with 10% FBS.

In certain embodiments, γ-secretase inhibitor XXI could be replaced with the Notch pathway inhibitor DAPT, DBZ.

In certain embodiments, BMP7, FGF19, and oncostatin M (OSM) were optional. Either one of them could be removed, and the cells were still able to differentiate into hepatocyte with lower efficiency.

2D Hepatocyte Differentiation

Hepatic stem cells were cultured on feeder for 7 to 10 days. After stem cells reach 50% to 70% confluence, cell culture medium was added with BMP4 20, 50, 100 ng/ml and Fgf2 10, 20, 50, 100 ng/ml for 3-5 days and change to hepatocytes differentiation medium to initiate hepatocyte differentiation. The medium was changed every 2-3 days for 14 days. Prolonged culture in hepatocyte differentiation medium could increase the hepatocyte maturation. The differentiated cells could be continued cultured for more than 30 days in Clonetics™ HMM™ Hepatocyte Maintenance Medium (HMM).

In certain embodiments, liver stem cells were seeded on feeders at high density 1×10⁵ cells/cm² in stem cell culture medium. When the liver stem cells reach confluency, the culture media is replaced with the differentiation media. Mature hepatocyte will form after 14 to 21 days (FIGS. 17A and 17B).

3D Hepatocyte Differentiation

Liver stem cells were cultured on feeders for 6 to 10 days. The cells are subsequently retrieved and seeded as single cells in ultra-low attachment cell culture dish at a density of 1×10⁵ cells/cm² in human liver stem cell culture medium.

In certain embodiments, cells was seeded on low attachment 96 well plate at 2-5×10⁴/well.

On the second day, the stem cells were cultured in liver stem cell medium with BMP4 20, 50, 100 ng/m and Fgf2 10,20, 50, 100 ng/ml for another 3-5 days to form sphere structures. Hepatocyte differentiation medium were used to culture the sphere structures in low attachment plate to initiate hepatocyte differentiation. Medium was changed every 2-3 days. The mature hepatocytes were derived in 8th to 14th days of differentiation. Prolonged culture in hepatocyte differentiation medium increased the 3D hepatocyte maturation. The 3D hepatocytes were cultured in differentiation medium as long as 30 days with medium changing every 2-3 days. The 3D hepatocyte could be maintained in Clonetics™ HMM™ Hepatocyte Maintenance Medium (HMM) for 2-3 months (FIG. 24).

Hepatocytes Air-Liquid Interface (ALI) Differentiation

Liver stem cells were plated on 3T3J2 feeders in transwells (Corning, 0.4 μm pore size, polyester membrane) at a density of 3×10⁴ cell/cm². The cells in transwells were cultured in liver stem cell medium for 7 to 10 days. The medium inside the inserts were removed and the medium outside the insert were changed to hepatocyte differentiation. The cells on air-liquid interface were cultured for another 14 days with medium changes every 2-3 days. In day 10 to 14, the mature hepatocyte were derived. Prolonged culture in hepatocyte differentiation medium could increase the hepatocyte maturation. The differentiated cells could be continued cultured for more than 30 days (FIG. 27).

All described hepatocyte differentiation methods produced functional human hepatocytes without fetal and immature hepatocyte markers expression such as AFP (except for hepatocytes derived from LSCs from hepatocarcinoma patients, which do express AFP). Differentiated hepatocytes had Cytochrome p450 drug metabolism function (FIG. 20), glycogen storage and LDL uptake function (FIG. 23). Currently the efficiency of 2D and 3D differentiation was around 80% to 90% (FIG. 18). The highest differentiation efficiency of 3D could reach 100% in certain individual 3D hepatocyte spheres (FIG. 24, FIG. 25). The 3D differentiated hepatocytes expressed the hepatocyte terminal differentiation markers PEPCK and TAT. Six major CYPs p450 family members had increased RNA expression (FIG. 21). CYP1A2, 2C9, 2B6, and 3A4/5 function was determined by metabolic assays. The hepatocytes also show drug induced response for CYP3A4 and CYP2C9 activity (FIG. 20B).

Although Hepatic stem cell differentiated hepatocyte displayed many features of primary adult hepatocyte, they are different in several aspects (Table 2). Liver stem cell differentiated hepatocyte (dHep) was smaller than adult primary hepatocyte (aHep) in cell size. aHep size is 2-10 times larger than dHep. Majority of the dHep are diploid with single nucleus, but a significant numbers of aHep are polyploid, and can also be binucleated. aHep CYPs function could only be maintained in vitro for 24-48 hours in cell culture, but dHep CYPs function could be maintained for more than 30 days (FIG. 24).

Example 4

Differentiation of Liver Stem Cells to Cholangiocytes

Biliary duct differentiation medium consisted of advanced F12/DMEM reduced serum medium (1:1)(Gibco. 12643), 10 mM HEPES (Gibco), 100U/ml Pen/Strep (Gibco), 2 mM L-Glutamine (Gibco), 1% N2 (Gibco), 2% B27 (Gibco), 10 ng/ml EGF (Millipore), 100 ng/ml Fgf10 (R&D).

Tgfβ inhibitor and Notch inhibitor were not present in the medium. The bile duct differentiation medium is Tgfβ inhibitor and Notch inhibitor free.

In certain embodiments, Tgfβ and Notch ligand jagged-1 were added in the differentiation medium to help bile duct forming. Either of them was optional.

Growth factor reduced matrigel was thawed one day before at 4° C. 50 ul of matrigel was put in one well of the 8 chamber slide. The chamber slides with matrigel were incubated at 37° C. Half an hour later, the matrigel solidified and formed dome shape and jelly like structure on each well. Liver stem cells were digested by 0.05% trypsin for 30 to 60 seconds. The liver stem cells were seeded in the growth factor reduced matrigel suspension at a density of 3-5×10⁴ cells/400 μl/well. After 3 to 5 days, when the sphere structures formed, the liver stem cell medium was changed to biliary duct differentiation medium. The differentiation medium was changed every 2 days. Cholangiocytes are form 14 days later.

The biliary duct differentiation method gave rise to biliary duct-like 3D structure (FIGS. 27, 28, 29A and 29B). This structure mimics a closed duct in which the cells are arranged in a sphere or tubular structure with an enclosed lumen or space surrounded by the cholangiocytes which have tight junctions between them. In some of the biliary duct-like structures mucus can be observed to be secreted into the lumen. All the cells stained positive for biliary markers KRT19 and KRT7 suggesting close to 100% differentiation efficiency (FIG. 29B). The cells were fully polarized with microvilli on the luminal apical part of the structures (FIG. 28). Nucleus in the cells were located near the basal membrane (FIG. 28). Tight junction marker ZO-1 was expressed between the cells (FIG. 29). The biliary duct organoids display organization that mimicked in vivo biliary duct structure.

The process of bile duct 3D differentiation can comprise of the following steps: placing extracellular matrix in a suitable container (such as 50-60 μl of matrigel on one well of 8 well chamber slides); solidifying the extracellular matrix (such as matrigel) to form a dome shape jelly-like structure in the suitable container (such as cell culture chamber); placing the liver stem cells (optionally with suitable digestion enzymes such as trypsin) on the extracellular matrix (such as seeding the liver stem cells on top of the matrigel); incubating the extracellular matrix and the liver stem cells and allowing the aggregated cells to form a sphere structure on top of the extracellular matrix (such as matrigel). Without wishing to be bound by theory, it is believed that the extracellular matrix (such as matrigel) supports cells aggregation and form 3D structure, which helps to initiate bile duct differentiation. Furthermore, it is believed that TGF-beta and other cytokine in the extracellular matrix (such as matrigel) facilitate the sphere structures to further differentiate into bile duct-like structure. Extracellular matrix (such as matrigel) supports the sphere structure formation and assists in the polarization of the sphere structure to further differentiate into bile duct-like structure. Although Hepatic stem cell differentiated cholangiocytes displayed many features of primary adult cholangiocytes, they are different in several aspects (Table 5). The LSC-derived cholangiocytes lack cuboidal cholangiocytes which have proliferative potential. No proliferation of LSC cholangiocytes was observed. While ECAD expression varies in the adult primary cholangiocyte, all the cholangiocyte in our culture expressed ECAD.

Example 5

Liver Stem Cells Obtained from Patients with Liver Diseases

Liver stem cells were derived not only from healthy liver donors, but also from patient with liver diseases (Table 1). We derived fatty liver stem cells from Non Alcoholic Fatty Liver Disease (NAFLD) patient HBV-infected cirrhotic liver patient and from a patient with hepatocellular carcinoma (HCC), from both tumor and adjacent healthy liver. We performed RNASeq gene expression analysis on the derived liver stem cells from these patients and from healthy donors. Our data showed that fatty liver stem cells were enriched in gene pathways consistent with the disease phenotype observed in disease liver in NAFLD patient (Table 3). Stem cells from NAFLD patient were enriched in cholesterol biosynthesis and leucine degradation genes compared to healthy and HBV infected cirrhotic liver stem cells. NAFLD patient also had high blood cholesterol and an amino acid imbalance phenotype (FIGS. 30A and 30B). Liver stem cells isolated from HCC tumor and tumor adjacent normal liver tissues were morphologically different even though they were derived using identical method and medium (FIG. 31). Single cell derived HCC liver stem cells were injected to NSG mice by intrasplenic injection. The transplanted mice developed HCC in the mouse liver (FIG. 31). Human HCC stem cells formed HCC tumor in mice and also express human specific albumin (FIG. 32A, 32B).

Example 6

Liver Regeneration

This example demonstrates that both liver stem cells and differentiated liver stem cells (dHep) rescued the liver cirrhosis phenotype when transplanted into a mice treated with thioacetamide to induce liver cirrhosis mice (FIG. 33A). The mice developed liver cirrhosis by continuing thioacetamide treatment for 2-3 months. Liver stem cells and liver stem cell differentiated dHep cells were transplanted into the mice by intrasplenic injection. After transplantation, the mice continued to receive drug treatment for another 3 months (FIG. 33A). Mouse liver functions were tested in the third month. Transplanted mice group had higher serum albumin than non-transplanted control group (FIG. 33B). Their liver functions were therefore partially rescued. The livers of mice receiving transplanted dHEP cells have less fibrosis and inflammation than control group (FIG. 35). dHep was repopulated in transplanted mouse liver (FIG. 36). Both liver stem cells and dHEP cells integrated into mouse liver tissue and expressed human specific albumin (FIG. 34,36. Table 4).

The liver stem cell (LSC) and their differentiated hepatocyte (dHep) and bile duct cells have the potential to treat liver cirrhosis caused by different liver diseases. In vitro derived autologous LSC, dHep and bile duct cells can be delivered to the same patient to rescue liver failure and reduce liver cirrhosis. LSC can be derived from the same patient and in vitro cultured for expansion. dHep and bile duct cells are in vitro differentiated from LSC. These stem cells and differentiated cells are autologous and will not induce transplant rejection in patients.

REFERENCES

-   1. Gebhardt R, Baldysiak-Figiel A, Krugel V, Ueberham E, Gaunitz F.     Hepatocellular expression of glutamine synthetase: An indicator of     morphogen actions as master regulators of zonation in adult liver.     Prog Histochem Cytochem. 2007; 41(4):201-66. Epub 2007 Feb. 8. -   2. Lee W. M. Drug-induced hepatotoxicity. N. Engl. J. Med. (2003)     349 474-485. -   3. Si-Tayeb K., Noto F. K., Nagaoka M., Li J., Battle M. A., Duris     C., North P. E., Dalton S., Duncan S. A. Highly efficient generation     of human hepatocyte-like cells from induced pluripotent stem cells.     Hepatology. 2010; 51:297-305. -   4. Si-Tayeb K1, Lemaigre F P, Duncan S A. Organogenesis and     development of the liver. Dev Cell. 2010 Feb. 16; 18(2):175-89. doi:     10.1016/j.devcel.2010.01.011. -   5. Zanger UM1, Schwab M. Cytochrome P450 enzymes in drug metabolism:     regulation of gene expression, enzyme activities, and impact of     genetic variation. Pharmacol Ther. 2013 April; 138(1):103-41. doi:     10.1016/j.pharmthera.2012.12.007. Epub 2013 Jan. 16. -   6. Schwartz RE1, Fleming HE2, Khetani SR3, Bhatia SN4. Pluripotent     stem cell-derived hepatocyte-like cells. Biotechnol Adv. 2014     March-April; 32(2):504-13. doi: 10.1016/j.biotechadv.2014.01.003.     Epub 2014 Jan. 16. -   7. Tabibian J H, Masyuk A I, Masyuk T V, O'Hara S P, LaRusso N F.     Physiology of Cholangiocytes. Comprehensive Physiology. 2013;     3(1):10.1002/cphy.c120019. doi:10.1002/cphy.c120019. -   8. Michalopoulos G K, DeFrances M C. Liver regeneration. Science     1997; 276:60-66. [PubMed: 9082986] -   9. Okabe M, Tsukahara Y, Tanaka M, et al. (2009) Potential hepatic     stem cells reside in EpCAM+ cells of normal and injured mouse liver.     Development 136, 1951-1960. -   10. B Wang, Self-renewing diploid Axin2+ cells fuel homeostatic     renewal of the liver. Nature. 2015 Aug. 13; 524(7564): 180-185. -   11. J Font Burgada et al. Hybrid Periportal Hepatocytes Regenerate     the Injured Liver without Giving Rise to Cancer, cell.2015.07.026 -   12. Schmelzer E, Zhang L, Bruce A, et al. (2007) Human hepatic stem     cells from fetal and postnatal donors. J Exp Med 204, 1973-1987. -   13. Melissa Baxter et al Phenotypic and functional analyses show     stem cell-derived hepatocyte-like cells better mimic fetal rather     than adult hepatocytes. J Hepatol. 2015 March; 62(3): 581-589. doi:     10.1016/j.jhep.2014.10.016

List of Abbreviations

CYP: Cytochrome p450; LGR5: Leucine-rich repeat-containing G-protein coupled receptor 5; EPCAM: Epithelial cell adhesion molecule; KRT19: Cyto-keratin 19; KRT7: Cyto-keratin 7; CYP3A4: Cytochrome P450, Family 3, Subfamily A, Polypeptide 4; CYP2C9: Cytochrome P450, Family 2, Subfamily C, Polypeptide 9; AFP: Alpha-Fetoprotein; HNF3B: Hepatocyte Nuclear Factor 3, Beta; HNF4A: Hepatocyte Nuclear Factor 4, Alpha; NAFLD: nonalcoholic fatty liver disease; NASH: nonalcoholic steatohepatitis; PSC: Primary sclerosing cholangitis; PBC: Primary biliary cirrhosis; DILI: drug induced liver injury; HCC: hepatocarcinoma; LSC: liver stem cell; IF: Immunofluorescence; E-CAD: E-Cadherin; KI67: Antigen KI-67; SOX9: SRY (Sex Determining Region Y)-Box 9; ESC: embryonic stem cell; CD24: Signal transducer CD24; PROM1: Prominin 1; FOXA3: Forkhead Box A3; FOXQ1: Forkhead Box Q1; ALB: Albumin; PROX1: Prospero Homeobox 1; FOXA2: Forkhead Box A2; qPCR: Quantitative polymerase chain reaction; FACS: Fluorescence-activated cell sorting; 2D: 2 dimensional; 3D: 3 dimensional; CTX: cholera enterotoxin; PEPCK: Phosphoenolpyruvate Carboxykinase 1; ZO1: Zona Occludens 1; eHep: ESC differentiated hepatocyte; dhep: LSC in vitro differentiated hepatocyte; PAS: Periodic acid Schiff; LDL: Low-density lipoprotein; TAT: Tyrosine Aminotransferase; ALI: air liquid interface; HBV: Hepatitis B virus; PCA: Principle component analysis; GSEA: Gene enrichment analysis; TA: Thioacetamide; IHC: immunohistochemistry; NSG:NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ; EHS: Engelberth-Holm-Swarm.

A83-01:3-(6-Methyl-2-pyridinyl)-N-phenyl-4-(4-quinolinyl)-1H-pyrazole-1-carbothioamide); SB431542: 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide; SB 216763 (3-(2,4-Dichlorophenyl)-4-(1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione), SB 415286: 4-[4-(1,3-benzodioxol-5-yl)-5-(2-pyridinyl)-1H-imidazol-2-yl]benzamide; CHIR 99021:6-[[2-[[4-(2,4-Dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2-pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile; CHIR 99021 trihydrochloride: 6-[[2-[[4-(2,4-Dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl)-2-pyrimidinyl]amino]ethyl]amino]-3-pyridinecarbonitrile trihydrochloride; MeBIO: (2′Z,3′E)-6-Bromo-1-methylindirubin-3′-oxime; TCS 2002: 2-Methyl-5-[3-[4-(methylsulfinyl)phenyl]-5-benzofuranyl]-1,3,4-oxadiazole; NSC 693868: 1H-Pyrazolo[3,4-b]quinoxalin-3-amine; TCS 21311: 3-[5-[4-(2-Hydroxy-2-methyl-1-oxopropyl)-1-piperazinyl]-2-(trifluoromethyl)phenyl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione; AR-A 014418: N-[(4-Methoxyphenyl)methyl]-N′-(5-nitro-2-thiazolyl)urea; 3F8: 5-Ethyl-7,8-dimethoxy-1H-pyrrolo[3,4-c]isoquinoline-1,3(2H)-dione; L803: Peptide KEAPPAPPQSP, A 1070722: 1-(7-Methoxyquinolin-4-yl)-3-[6-(trifluoromethyl)pyridin-2-yl]urea; TC-G 24: N-(3-Chloro-4-methylphenyl)-5-(4-nitrophenyl)-1,3,4-oxadiazol-2-amine; TWS 119: 3-[[6-(3-Aminophenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]oxyphenol ditrifluoroacetate; L803-mts: peptide GKEAPPAPPQSP; FRAT: frequently rearranged in advanced T-cell lymphomas; T3: 3,3′-5-triiodo-1-thyronine; T4: (S)-thyroxine; PTH: parathyroid hormone; NECA: 5′-(N-ethylcarboxamido)-adenosine; cAMP: cyclic adenosine monophosphate; NAC: N-Acetyl-Cysteine; BMP: Bone Morphogenetic Protein; HGF: Hepatocyte Growth Factor; FGF: Fibroblast Growth Factor; IRBs: Institutional Review Boards; ALI: air-liquid interface; LY 364947: (4-[3-(2-pyridinyl)-1H-pyrazol-4-yl]-quinoline; SD 208: (2-(5-Chloro-2-fluorophenyl)pteridin-4-yl]pyridin-4-yl-amine); D4476: (4-(4-(2,3-Dihydrobenzo[1,4]dioxin-6-yl)-5-pyridin-2-yl-1H-imidazol-2-yl)benzamide); GW 788388: (4-[4-[3-(2-Pyridinyl)-1H-pyrazol-4-yl]-2-pyridinyl]-N-(tetrahydro-2H-pyran-4-yl)-benzamide); SB 505124: (2-(5-Benzo[1,3]dioxol-5-yl-2-tert-butyl-3H-imidazol-4-yl)-6-methylpyridine), SB 525334: (6-[2-tert-Butyl-5-(6-methyl-pyridin-2-yl)-1H-imidazol-4-yl]-quinoxaline); RepSox: (E-616452; or 2-[3-(6-Methyl-2-pyridinyl)-1H-pyrazol-4-yl]-1,5-naphthyridine); R 268712 (4-[2-Fluoro-5-[3-(6-methyl-2-pyridinyl)-1H-pyrazol-4-yl]phenyl]-1H-pyrazole-1-ethanol)

Deposit Statement

Cultures of the liver stem cells (cell line L1-5 hLSC) and differentiated hepatocytes (cell line RFPL1-5 dHep) described herein were deposited on 8 Mar. 2017 under terms of the Budapest Treaty of 1977 with the European Collection of Authenticated Cell Cultures (Public Health England, Porton Down, Salisbury, SP4 0JG, UK), and given the patent deposit designation numbers 17030801 and 17030802, respectively. The microorganism deposit was made under the provisions of the “Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure.” All restrictions on the availability to the public of these deposited microorganisms will be irrevocably removed upon issuance of a patent based on this application. For the purposes of this disclosure, any isolate having the identifying characteristics of the deposited cells, including subcultures and variants thereof having the identifying characteristics and activity as described herein, are included.

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, sequence accession numbers, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

TABLE 1 Derived liver diseased cell lines Personalized Single cell Donor and Stem Cell derived LSC Successful subject (patient) (Total number lines of each Isolation recruitment of subjects) subject Rate Healthy Donor 7 3/subject 83.3%   Patient HIV infection 7 3/subject 90% with liver Alcohol induced 1 3/subject cirrhosis cirrhosis Fatty Liver 3 3/subject With liver Subject has 3 3/subject 20% cancer Hepatitis B Virus (HCC) infection

Table 1: LSC was isolated and expanded from liver diseased patient and healthy donor's liver tissue. Each subject or patient have at least 3 individual single cell formed lines. The successful rate of isolation LSC from clinical patient were indicated. This table shows that patient specific LSC were derived. Collected disease related stem cells could be banked as a resource for liver disease study.

TABLE 2 Comparison between LSC differentiated hepatocyte and primary hepatocyte. dHep Primary hepatocyte Cell Size Smaller Larger, about 2-10x larger than dHep Nucleus Single nucleus, diploid Binucleate and polyploid cells common CYP functional High CYPs activity, but Full CYPs family functional activity not more than 70%, 80%, activity when freshly isolated 90% of freshly isolated primary hepatocyte Maintenance in Could be maintained for Cannot be maintained in culture more than 30 days in culture. Full CYP functional culture, retaining CYPs activity cannot be retained for functions more than about 24-48 hours post-isolation from liver tissue

TABLE 3 LSC was derived from both healthy liver donor and liver disease subjects. LSCs could be derived from the following liver diseases: Metabolic disease Nonalcoholic fatty liver disease (NAFLD) Nonalcoholic steatohepatitis (NASH) Autoimmune disease primary sclerosing cholangitis (PSC) primary biliary cirrhosis (PBC) Infectious disease Hepatitis A, B, C virus infected liver cirrhosis Drug induced acute and Drug induced liver injury (DILI) chronic liver failure Alcoholic liver cirrhosis Liver cancer Hepatocellular carcinoma (HCC) cholangiocarcinoma

TABLE 4 Partially rescued mouse liver function by LSC in vitro differentiated hepatocyte (dHEP). Liver Function test sample *PT (sec) ALB (g/L) Control 1 12.7 12.2 Control 2 11.6 16.55 Control 3 11.4 16.77 Transplanted-1 11 28.61 Transplanted-2 10.8 45.41 Transplanted-3 10.9 21.94 Transplanted-4 11.1 32.08 Transplanted-5 10.7 33.11 Transplanted-6 10.9 30.63 *PT time: Prothrombin time (PT) is a blood test that measures how long it takes blood to clot.

Table 4.

Mouse liver function test table. Alb level was significantly higher in the transplanted group than the control group. It indicated in vitro LSC differentiated hepatocyte (dHep) partially rescued liver function in the TA induced liver cirrhosis mouse model. This figure shows that dHep partially rescued mouse liver function in liver cirrhosis mouse model.

TABLE 5 Comparison between LSC differentiated cholangiocyte and primary cholangiocyte. LSC differentiated cholangiocyte Primary cholangiocyte Function Able to secrete mucus Able to secrete mucus Ciliary structure Have ciliary structure Have ciliary structure Cell shape Only columnar in shape Cuboidal in shape in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts. Proliferative No proliferative potential Cuboidal cholangiocytes potential have proliferative potential Cell surface Expressed E-cadherin Varied expression of markers E-cadherin 

What is claimed is:
 1. A method of treating a subject having liver disease, comprising transplanting a human liver stem cell comprising the following characteristics into the liver of the subject: (i) expresses at least 1, 2, 3 or 4 of the protein markers selected from SOX9, HNF4α, HNF3β, and EPCAM; (ii) expresses low levels of KRT19 protein, (iii) does not express detectable protein levels of KRT7 or AFP; and (iv) does not have a polarized cell phenotype, wherein the transplanted cell repopulates the liver of the subject, thereby treating the liver disease.
 2. The method of claim 1, wherein the liver disease is selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure, and liver cancer.
 3. The method of claim 1, wherein the liver stem cell further expresses 1, 2, 3, 4, or 5 protein markers selected from CD24, PROM1, FOXA3, FOXQ1 and ECAD.
 4. The method of claim 1, wherein the characteristics of the stem cell are maintained in long-term culture, and comprise a normal karyotype after 19 passages in culture.
 5. The method of claim 1, wherein the liver stem cell is a human fetal liver stem cell.
 6. The method of claim 1, wherein the liver stem cell is isolated from a healthy human subject.
 7. The method of claim 1, wherein the liver stem cell is isolated from a human subject with a liver disease, wherein the liver disease is selected from the group of metabolic disease, autoimmune disease, infectious disease, drug induced acute and chronic liver failure. 